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openmm

OpenMM GPU acceleration interface to CHARMM This module describes the interface of CHARMM with the OpenMM development platform for GPU accelerated simulations. CHARMM is compatible with OpenMM versions 6.3 and greater. The current interface supports molecular dynamics on CUDA or OPENCL supported graphical processing units (GPUs). For a full list of hardware on which the OpenMM libraries should run, see the OpenMM website (https://simtk.org/home/openmm). The OpenMM methods are free and available as pre-compiled libraries or source form. In addition, one needs the NVIDIA drivers and CUDA toolkit installed on the machine - please see OpenMM documentation for the basic procedures to set-up and install these components, as well as which versions are required. The CHARMM/OpenMM interface is under continuing development with new CHARMM features being added all of the time. The current implementation supports dynamics and energy calculations for periodic and non-periodic systems using cutoffs, nocutoffs (for finite systems), and PME/Ewald and cutoffs for periodic systems. Periodic systems supported are only orthorhombic (a,b,c, alpha=beta=gamma=90. Only Leapfrog Verlet integration and Langevin dynamics are supported. Constant temperature molecular dynamics is also supported through the Andersen heatbath method in the OpenMM module. Additionally, constant pressure, constant temperature dynamics are available using MC sampled barostat. Finally, we have provided access to the variable timestep Verlet (Leapfrog) and Langevin integrators implemented in the OpenMM module. SHAKE is supported as are all of the CHARMM forcefields, e.g., CMAP. Special Notice: The CHARMM/OpenMM interface is an evolving interface with the OpenMM accelerated dynamics engine for GPU accelerated molecular dynamics (See the News at www.charmm.org for a discussion of the benchmarks and their performance). The functionality present through the current CHARMM interface has been released prior to "aging" in the CHARMM developmental version for a year because of the important performance enhancements in provides through GPU acceleration. The interface and associated modules have been well tested, but are likely to contain yet undiscovered limitations, compared with the full functionality in CHARMM. Additionally, we note that this code operates in single precision as default, which may not be acceptable for all applications. However, with the release of OpenMM 5.0 double and mixed precision models are available. At present, the CHARMM/OpenMM interface accommodates molecular dynamics with and without periodic boundary conditions, using all of the current CHARMM force fields, and in NVE, NVT and NPT ensembles - although not using the same methods of achieving these as in the rest of CHARMM. Users are forewarned to carry out some pre-testing on their system prior to initiating long runs on GPUs. As new features and methods are added to the documentation. * Setup / Setting up to use/compile CHARMM/OpenMM * Usage / Usage and functional support of CHARMM/OpenMM * Multi-GPU / Using multiple GPUs and platforms * Block-OpenMM Running Block calculations on the GPU * GBSAOBC2-OpenMM Running GBSA OBC2 Generalized Born Model OpenMM * Examples / Examples of CHARMM/OpenMM usage
Top SETTING UP AND BUILDING CHARMM/OPENMM ===================================== To build CHARMM with the OpenMM interface to enable GPU accelerated molecular dynamics one needs to first install the appropriate GPU drivers and software support, e.g., NVIDIA drivers and CUDA toolkit. Additionally, the OpenMM libraries need to be installed. Please see the OpenMM web pages and documentation to accomplish this procedure (https://simtk.org/home/openmm). OpenGL header files may need to be installed. For example, for Debian and related Linux distributions. One may need to install the package mesa-common-dev if it is not already installed. Setup necesssary environment variables for load library and OpenMM path: The following environment variables need to be setup: OPENMM_PLUGIN_DIR and the library path. Assuming OpenMM has been installed in it's default directory (/usr/local/openmm), then set the following environment variable: Mac OSX or Linux bash shell: export OPENMM_PLUGIN_DIR=/usr/local/openmm/lib/plugins csh shell: setenv OPENMM_PLUGIN_DIR /usr/local/openmm/lib/plugins These should be added to your .bashrc or .cshrc to ensure they are always setup. Additionally, one needs to tell the loader where the OpenMM libraries are installed. This differs on Linux versus Mac OSX systems because of static versus dynamic load library uses on these two OSs. Linux (bash): export LD_LIBRARY_PATH=/usr/local/openmm/lib:$OPENMM_PLUGIN_DIR:$LD_LIBRARY_PATH Linux (csh): setenv LD_LIBRARY_PATH /usr/local/openmm/lib:$OPENMM_PLUGIN_DIR:$LD_LIBRARY_PATH Mac OSX (bash): export DYLD_LIBRARY_PATH=/usr/local/openmm/lib:$OPENMM_PLUGIN_DIR:$DYLD_LIBRARY_PATH Max OSX (csh): setenv DYLD_LIBRARY_PATH /usr/local/openmm/lib:$OPENMM_PLUGIN_DIR:$DYLD_LIBRARY_PATH OpenMM anisotropic barostat, GBSW and PHMD functionality are also available as OpenMM plugins. When CHARMM is built using install.com, the plugins are installed in the directory <CHARMM root directory>/lib/<CHARMM host>/openmm_plugins (for example <CHARMM root directory>/lib/osx/openmm_plugins). When CHARMM is built using CMake, the plugins are install in the directory <CHARMM root directory>/lib. There is no longer any need to set CHARMM_PLUGIN_DIR at build or run time unless you have copied the CHARMM's plugins to a new directory. In this case, you may need to add the new directory to (DY)LD_LIBRARY_PATH and set the environment variable CHARMM_PLUGIN_DIR to the new location. INSTALLING CHARMM/OpenMM ======================== Installing CHARMM with the OpenMM interface is straightforward on Linux and Mac OSX: Setup necesssary environment variables: Set OPENMM_PLUGIN_DIR as described above, and set CUDATK to the location of the CUDA toolkit. Assuming OpenMM and CUDA have been installed in their default directories (/usr/local/openmm and /usr/local/cuda respectively), then set the following environment variables: Mac OSX or Linux bash shell: export OPENMM_PLUGIN_DIR=/usr/local/openmm/lib/plugins export CUDATK=/usr/local/cuda csh shell: setenv OPENMM_PLUGIN_DIR /usr/local/openmm/lib/plugins export CUDATK=/usr/local/cuda These should be added to your .bashrc or .cshrc to ensure they are always setup. Linux / Intel compilers install.com em64t openmm Linux / GCC compilers install.com gnu openmm Mac OSX / Intel compilers install.com osx ifort openmm Mac OSX / GCC compilers install.com osx gfortran openmm The OpenMM anisotropic barostat, GBSW and PHMD plugins are available for use by default. Note: At present we are supporting features for OpenMM 6.3 and 7.0 releases. These releases may provide slightly different interfaces to Cuda-based computations and precision. See comments below for more details.
Top USAGE and IMPLEMENTATION ======================== USAGE: add keyword omm to dynamics command dynamc or to energy call (via the energy or gete commands energy . For dynamics, this gives you the default Verlet Leapfrog integrator with timestep specified in the dynamics command. For energy/gete calls, you get all energy terms that are active with the non-bonded and bonded terms being computed on the GPU. One can also include the various options noted below: SUMMARY OF OPENMM COMMANDS ========================== OMM [ openmm-control-spec ] openmm-control-spec on Sets omm_active to true and tells CHARMM all subsequent calls to energy, dynamics or minimization will use OpenMM interface for calculation of supported energies and forces. OpenMM context will be created later as needed off Sets omm_active to false but retains any OpenMM context already created clear Sets omm_ative to false and destroys the OpenMM Context serialize [system, state, integrator] [unit <unit #>] Serializes the given OpenMM object: system (the default), state, or integrator as an XML string. The string is output to OUTU in the case of missing [unit <unit #>] and is output to unit <unit #> otherwise platform [cuda,reference,opencl,cpu] Provides platform and device level control from inside precision [single, mixed, double] CHARMM command language. deviceid [<specify device IDs to use>] setting up GBSA OBC2 gbsa [<gboff/gbon> uueps <real> vveps <real>] Enable gbsa module (subsequently turn it off w/ gboff or on w/ gbon) set dielectric for solute (uueps, default 1) or solvent (vveps, default 78.5). Dynamics keyword options in CHARMM/OpenMM interface keyword default action ========================================================================================= omm false - dynamics keyword to access openMM interface langevin false - dynamics keyword to turn on Langevin integration andersen false - dynamics keyword to turn on Andersen heatbath prmc false - dynamics keyword to turn on MC barostat variable false - dynamics keyword to use variable timestep md gamma 5.0 - Langevin friction coefficient in ps^-1 colfrq 1000 - Andersen heatbath coupling constant ps^-1 pref 1.0 - MC barostat reference pressure in atmospheres prxx, pryy, przz 1.0 - MC barostat reference pressure in atmospheres tens 0.0 - MC barostat reference surface tension (in dynes/cm^2) iprsfrq 25 - MC barostat sampling frequency vtol 1e-3 - Variable timestep error tolerence NOTE: Coordinates, velocities and restart files can be written every NSAVC, NSAVV, ISVFRQ timesteps to files specified by IUNCRD, IUNVEL and IUNWRI. Restarts can be used specifying RESTSRT in the dynamics command with IUNREA also specified, like normal CHARMM runs. WARNING: At present the energy file is not written, since OpenMM only returns the total energies (TOTE, TOTKE, EPOT and TEMP) and VOLUME. Constant Temperature Dynamics ============================= omm langevin gamma <real> - runs Langevin dynamics with friction coefficient gamma (ps^1) <5.0> at a temperature given by finalt in dynamics command. omm andersen colfreq <integer> - runs constant T with Andersen collision frequency colfrq <1000> at temperature given by finalt in dynamics command Constant Pressure/Constant Temperature Dynamics =============================================== Using either of the integrators noted above, one can run MC barostat-ed molecular dynamics by adding: omm langevin gamma <real> prmc pref <real> iprsfrq <integer> - runs Langevin dynamics with <5.0> <1.0> <25> barostat with a reference pressure of pref atmospheres and MC volume move attempted every iprsfq steps. In addition, we have implemented a varient of the anisortopic barostat that enables constant surface tension, constant surface area and related ensembles to be simulated. The freedom in changing the size/shape of the box is related to the crystal space group chosen as well as the type of barostat. The relevant commands are: omm prmc przz <real> iprsfrq <integer> - runs constant normal pressure and constant surface area omm prmc prxx <real> pryy <real> iprsfrq <integer> - constant z dimension, constant pressure in independent tangential x, y dimensions omm prmc tens <real> iprsfrq <integer> - constant surface tension and constant volume x,y degrees of freedom coupled to surface tension, z changes to maintain constant volume omm prmc tens <real> przz <real> iprsfrq <integer> - constant surface tension and normal pressure Variable Timestep Molecular Dynamics ==================================== OpenMM has implemented a bounded error estimate driven variable timestep integration scheme in which the size of the timestep is bounded by a specified error that would be associated with the explicit Euler integrator. The timestep is chosen to satisfy the following relationship error = dt^2 Sum_i ( |f_i|/m_i ), where error is the desired maximum error in the step, given the current forces. From the user-supplied error, the timestep follows from dt = sqrt( error / Sum_i ( |f_i|/m_i ) ) Adding variable_timestep vtol <real> (default 1.0e-3) uses a variable timestep version of the above integrators (Langevin or Leapfrog). One can run NVE dynamics with Leapfrog as well, but this may be not useful. One can also use the variable timestep algorithms with the barostat. Energy Computations =================== Energy terms supported through the CHARMM/OpenMM interface for computation on the GPU include: BOND ANGL UREY DIHE IMPR VDW ELEC IMNB IMEL EWKS EWSE EWEX, HARM and ETEN. However, these are returned from the CHARMM/OpenMM interface as just ENER, i.e., the sum of the components. One can evaluate the individual components through use of the SKIPE commands. ================= The CHARMM/OpenMM interface supports a subset of the CONS HARM harmonic restraints. Speciically, the default ABSOLUTE restraints with XSCALE=YSCALE=ZSCALE=1 are supported. The COMP, WEIGHT and MASS keywords associated with this restraint are also supported (see cons and testcase c37test/3ala_openmm_restraints.inp) The CHARMM/OpenMM interface supports the CONS RESDistance restraints. (see cons and testcase c39test/omm_resdtest.inp) The CHARMM/OpenMM interface supports the CONS DIHEdral restraints. (see cons and testcase c39test/omm_consdihe.inp) The CHARMM/OpenMM interface can carry-out energy calculations that combine the forces for energy terms computed on the GPU (non-bonded (VDW/ELEC) and bonded (BOND, ANGL, DIHE, IMPHI) with those from other CHARMM functionality. At present, aside from doing a static energy/force evaluation, one cannot use it is planned that we will support this functionality in the future). NOTE: When using single precision arithmetic on the GPU, long NVE simulations may have an energy drift on the order of 10^-2 * KBOLTZ * T / NDEGF per nanosecond. However, with the release of OpenMM 5.0, both mixed and double precision models are available in both CUDA and OpenCL. As noted in the overview above, the CHARMM/OpenMM supports "no frills" molecular dynamics for periodic and non-periodic systems. For non-periodic systems cutoffs and no-cutoffs are supported. For cutoff based methods a reaction field can be utilized. This is also true for periodic systems that don't employ PME/Ewald methods. The cutoff method is keyed to the value of the energy-related cutoff CTOFNB. If CTOFNB > 990 it's assumed that no cutoffs are to be used and OpenMM computes all interactions for non-periodic systems. If CTOFNB < 990, and other truncation methods (set note below) are not specified then the solvent reaction field is used with a cutoff switch such that the electrostatic energy for atom pair ij, u_ij, is given by: q_i*q_j / 1 \ u_ij = ---------- .| ---- + k_rf*r^2 -c_rf | 4*pi*eps_0 \ r_ij / k_rf = (eps_solvwnt - 1)/(2*eps_solvent+1)/(r_cutoff)^3 c_rf = (3*eps_solvent)/(2*eps_solvent+1)/(r_cutoff) where r_cutoff is the cutoff distance (CTOFNB) and eps_solvent is the dielectric constant of the solvent. If eps_solvent >> 1, this causes the forces to go to zero at the cutoff. The CHARMM/OpenMM Generalized solvent reaction field can also be specified on any nonbond/energy/dynamic command as: energy omrf omrx <value> - default 1 Energy based cutoff methods ============================ Other energy based methods have recently been implemented. The CHARMM/OpenMM interface now supports the folowing combinations of van der Waals and electrostatic methods: Supported combinations of energy methods ---------------------------------------- **pme/ewald <specification> ctonnb <value> ctofnb <value> vatom vswitch/vfswitch *noewald atom switch vatom vswitch ctonnb <value> ctofnb <value> *noewald atom switch vatom vfswitch ctonnb <value> ctofnb <value> *noewald atom fswitch vatom vfswitch ctonnb <value> ctofnb <value> *noewald atom fshift vatom vswitch ctonnb <value> ctofnb <value> *noewald atom fshift vatom vfswitch ctonnb <value> ctofnb <value> *noewald atom omrxfld vatom vswitch/vfswitch ctonnb <value> ctofnb <value> OpenMM now supports a vdW switching function pf the form S = 1 - 6x^5 + 15x^4 - 10x^3 where x = (r-r_switch)/(r_cutoff - r_switch) and r_cutoff = ctofnb and r_switch = ctonnb. Also supported is the long range vdW correction that is keyed from the LRC command Summary of supported non-bond truncation methods: For van der Waals: VSWITCH, VFSWITCH, OMSW LRC For electrostatics: SWITCH, FSWITCH, FSHIFT, OMRF [OMRX <RxnFld_dielectric (default 1) >] *Note, non-Ewald/PME calculations are supported for periodic and non-periodic systems. **Note, see Ewald/PME discussion below. Ewald and PME support --------------------- This is deprecated, the CHARMM/OpenMM Interface now supports direct input of Kappa, fftx, ffty, fftz from CHARMM energy/dynamic/nonbond command for PME-based Ewald. Ewald and PME-based Ewald are both implemented. With PME-based Ewald the OpenMM interface employs the cutoff (CTOFNB), the box length, and an estimated error desired for the long-range electrostatic forces to determine the number of number of grid points for the PME calculations, FFTX, FFTY and FFTZ. However, to maintain consistency with CHARMM, the the error estimate and KAPPA. Thus, KAPPA as set in the CHARMM energy/nonbond or dynamics command may be over-ridden to ensure that FFTX(Y,Z) is maintained as requested. The error estimate is defined as delta and is related to KAPPA via the relaitonship delta = exp[-(KAPPA*CUTNB)^2) (1) In the current implementation, this relationship in the form KAPPA = Sqrt(-ln(2*delta))/CUTNB (2) is combined with FFTX(Y,Z) = 2*KAPPA*box_x(y,z)/(3*delta^(1/5)) (3) to eliminate KAPPA and is solved (via bisection) for a delta value that will yield the user provided values of FFTX(Y,Z) and KAPPA is determined from the relationship (2) above.
Top Control over the number of GPU devices one uses, the platform for GPU-based computations and the precision model is available through environment variables Environment variable Setting Effect OPENMM_DEVICE 0/1/0,1 Use device 0/1/0 and 1 (parallel) OPENMM_PLATFORM OpenCL/CUDA/Reference Use OpenMM platform based on OpenCL/Cuda/Reference(CPU) OPENMM_PRECISION single/mixed/double Do calculations in single (fastest), mixed or double precision (slowest) on platform CUDA_COMPILER path to cuda compiler nvcc (usually /usr/local/cuda/bin) Note: OpenMM chooses a default platform based on a guess for best performance if not is specified with the environment variable. Also, the platform Reference is a cpu-based platform for testing/validation purposes. Finally, the different precision models are not supported in OpenMM 4.1.1 (only single precision). Note: As of this release (02/15/2013) there is an issue with OpenCL on Mac OSX 10.7.8 and beyond, the OpenMM team and Apple are discussing these problems, and there will hopefully be resolution soon. Example (C-shell) setenv OPENMM_DEVICE 0,1 # Use both GPU devices Note: OpenMM 4.1.1 supports parallel calculations (0,1) only for platform OpenCL. OpenMM 5.0 adds parallel support for platform CUDA.
Top USING BLOCK IN CHARMM/OPENMM ============================ Many features of the CHARMM Block facility have been implemented on the GPU using the CHARMM/OpenMM interface. However, this has been done with some restrictions on the manner in which the interaction scaling is done. Block is used as detailed in the Block documentaiton for setting up the scaling of different terms. As with its implementation in CHARMM, one can scale the vdW, elec, bond, angle, dihed, impr terms independent of one another, although negative values of the block coefficients are not allowed due to a limitation in the manner in which the scaling is implemented. (Scaling is implemented by scaling corresponding force constants as the system is being set-up, this the affected bond, angle, dihedral and improper force constants are scaled by the block coefficient. The charges of atoms in a given block are also scaled by their block coefficient and the L-J emin value is scaled by the block coefficient squared, such that when the standard combination rules are applied the scaling of the interaction is by the block coefficient to the first power. The intra-block terms are treated differently for vdW and elec to ensure they match the CHARMM energies.) The rmla command to remove specific terms from the block scaling also works as it does in CHARMM. This implementaiton is fully suitable for running TI calculations or TP calculations. The trajectories generated at a particular lambda value can be post-processed either using the GPU-based CHARMM/OpenMM machinery, in which case the restrictions noted above apply and two separate passes must be carried out to get the "reactant" and "product" energies needed to construct the TI integratnd or the TP free energy increment. Alternatively, except if the OpenMM reaction field was employed, the trajectories can be post-processed using the the CHARMM Block facility as detailed in block.doc (see block ).
Top USING GBSA OBC2 IN CHARMM/OPENMM ================================ OpenMM provides the facility to implement the GBSA OBC2 model from Onufriev, Bashford and Case. This interface has been "opened" for use through the CHARMM/OpenMM interface. The relevant parameters to run these calculations are the inherent atomic radii and scaling constants. These parameters for protein atoms contained in the par/top_all36_prot models have been incorporated into the file toppar/openmm_gbsaobc2/charmm_all36_prot_gbsaobc.str. Streaming this file just before calling gbsa in the CHARMM/OpenMM interface puts the radii and scale factors into the wmain and wcomp arrays, respectively, making the subsequent call now prepared to upload the data to the CHARMM/OpenMM interace and thus run Generalzied Born calculations through the interface. A few support files are also included to 1) enable one to run the serialized CHARMM/OpenMM setup through the python API in OpenMM (see file tool/OpenMMFiles/omm_gbsaobc-test.py) and 2) enable one to extract radii and scaling factors for other Amber force fields (using the OpenMM supplied xml files for those force fields that reside in OpenMMn.nn-Mac/python/simtk/openmm/app/data/) using the awk script getff.awk (see file tool/OpenMMFiles/getff.awk). See usage Test case: test/c39test/omm_gbsaobc_streamn-test.inp
Top EXAMPLES ======== Molecular dynamics using NVE with PME in a cubic system (from JACS Benchmark): set nsteps = 1000 set cutoff = 11 set ctofnb = 8 set ctonnb = 7.5 set kappa = 0.3308 ! Consistent with cutofnb and fftx,y,z calc cutim = @cutoff ! Dimension of a box set size 62.23 set theta = 90.0 ! Dimension of a box Crystal define cubic @size @size @size @theta @theta @theta crystal build cutoff @cutim noper 0 image byseg xcen 0.0 ycen 0.0 zcen 0.0 select segid 5dfr end image byres xcen 0.0 ycen 0.0 zcen 0.0 select segid wat end ! turn on faster options and set-up SHAKE faster on energy eps 1.0 cutnb @cutoff cutim @cutim - ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 shake fast bonh tol 1.0e-8 para set echeck = echeck -1 open unit 20 write form restart.res ! Run NVE dynamics, write restart file calc nwrite = int ( @nsteps / 10 ) ! Run dynamics in periodic box dynamics leap start timestep 0.002 - nstep @nsteps nprint @nwrite iprfrq @nwrite isvfrq @nsteps iunwri 20 - firstt 298 finalt 298 - ichecw 0 ihtfrq 0 ieqfrq 0 - iasors 1 iasvel 1 iscvel 0 - ilbfrq 0 inbfrq -1 imgfrq -1 @echeck bycb - eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 ntrfq @nsteps - !PME omm ! Just turn on openMM, get Leapfrog Verlet, NVE ! Restart dynamics from current file ! Run dynamics in periodic box dynamics leap restart timestep 0.002 - nstep @nsteps nprint @nwrite iprfrq @nwrite isvfrq @nsteps iunwri 20 iunrea 20 - firstt 298 finalt 298 - ichecw 0 ihtfrq 0 ieqfrq 0 - iasors 1 iasvel 1 iscvel 0 - ilbfrq 0 inbfrq -1 imgfrq -1 @echeck bycb - eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 ntrfq @nsteps - !PME omm ! Just turn on openMM, get Leapfrog Verlet, NVE !!!!!!!!!!!!!!!!!!!LANGEVIN HEATBATH NVT!!!!!!!!!!!!!!!!!!!!! ! Run NVT dynamics with Langevin heatbath, gamma = 10 ps^-1 ! Run dynamics in periodic box dynamics leap start timestep 0.002 - nstep @nsteps nprint @nwrite iprfrq @nwrite isvfrq @nsteps iunwri 20 - firstt 298 finalt 298 - ichecw 0 ihtfrq 0 ieqfrq 0 - iasors 1 iasvel 1 iscvel 0 - ilbfrq 0 inbfrq -1 imgfrq -1 @echeck bycb - eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 ntrfq @nsteps - !PME omm langevin gamma 10 ! turn on openmm, set-up Langevin ! Run variable timestep Langevin dynamics with error tolerance of 3e-3 ! Run dynamics in periodic box dynamics leap start timestep 0.002 - nstep @nsteps nprint @nwrite iprfrq @nwrite isvfrq @nsteps iunwri 20 - firstt 298 finalt 298 - ichecw 0 ihtfrq 0 ieqfrq 0 - iasors 1 iasvel 1 iscvel 0 - ilbfrq 0 inbfrq -1 imgfrq -1 @echeck bycb - eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 ntrfq @nsteps - !PME omm langevin gamma 10 variable vtol 3e-3 ! turn on openmm, set-up variable ! timestep Langevin dynamics !!!!!!!!!!!!!!!!!!!LANGEVIN HEATBATH/MC BAROSTAT NPT!!!!!!!!!!!!!!!!!!!!! ! Run NPT dynamics with Langevin heatbath, gamma = 10 ps^-1 ! Run dynamics in periodic box dynamics leap start timestep 0.002 - nstep @nsteps nprint @nwrite iprfrq @nwrite isvfrq @nsteps iunwri 20 - firstt 298 finalt 298 - ichecw 0 ihtfrq 0 ieqfrq 0 - iasors 1 iasvel 1 iscvel 0 - ilbfrq 0 inbfrq -1 imgfrq -1 @echeck bycb - eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 ntrfq @nsteps - !PME omm langevin gamma 10 - ! turn on openmm, set-up Langevin mcpr pref 1 iprsfrq 25 ! set-up MC barostat at 1 atm, move attempt / 25 steps ! Run variable timestep Langevin dynamics with error tolerance of 3e-3 ! Run dynamics in periodic box dynamics leap start timestep 0.002 - nstep @nsteps nprint @nwrite iprfrq @nwrite isvfrq @nsteps iunwri 20 - firstt 298 finalt 298 - ichecw 0 ihtfrq 0 ieqfrq 0 - iasors 1 iasvel 1 iscvel 0 - ilbfrq 0 inbfrq -1 imgfrq -1 @echeck bycb - eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 ntrfq @nsteps - !PME omm langevin gamma 10 variable vtol 3e-3 - ! turn on openmm, set-up variable - ! timestep Langevin dynamics mcpr pref 1 iprsfrq 25 ! set-up MC barostat at 1 atm, move attempt / 25 steps !!!!!!!!!!!!!!!!!!!ANDERSEN HEATBATH NVT!!!!!!!!!!!!!!!!!!!!! ! Run NVT dynamics with Andersen heatbath, collision frequency = 250 ! Run dynamics in periodic box dynamics leap start timestep 0.002 - nstep @nsteps nprint @nwrite iprfrq @nwrite isvfrq @nsteps iunwri 20 - firstt 298 finalt 298 - ichecw 0 ihtfrq 0 ieqfrq 0 - iasors 1 iasvel 1 iscvel 0 - ilbfrq 0 inbfrq -1 imgfrq -1 @echeck bycb - eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 ntrfq @nsteps - !PME omm andersen colfrq 250 - ! turn on openmm, set-up Andersen mcpr pref 1 iprsfrq 25 ! set-up MC barostat at 1 atm, move attempt / 25 steps ! Run variable timestep Leapfrog w/ Andersen heatbath and error tolerance of 2e-3 ! Run dynamics in periodic box dynamics leap start timestep 0.002 - nstep @nsteps nprint @nwrite iprfrq @nwrite isvfrq @nsteps iunwri 20 - firstt 298 finalt 298 - ichecw 0 ihtfrq 0 ieqfrq 0 - iasors 1 iasvel 1 iscvel 0 - ilbfrq 0 inbfrq -1 imgfrq -1 @echeck bycb - eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 ntrfq @nsteps - !PME omm andersen colfrq 250 variable vtol 3e-3 ! turn on openmm, set-up variable ! timestep Langevin dynamics !!!!!!!!!!!!!!!!!!!ANDERSEN HEATBATH/MC BAROSTAT NPT!!!!!!!!!!!!!!!!!!!!! ! Run NPT dynamics with Andersen heatbath, collision frequency = 250 ! Run dynamics in periodic box dynamics leap start timestep 0.002 - nstep @nsteps nprint @nwrite iprfrq @nwrite isvfrq @nsteps iunwri 20 - firstt 298 finalt 298 - ichecw 0 ihtfrq 0 ieqfrq 0 - iasors 1 iasvel 1 iscvel 0 - ilbfrq 0 inbfrq -1 imgfrq -1 @echeck bycb - eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 ntrfq @nsteps - !PME omm andersen colfrq 250 - ! turn on openmm, set-up Andersen mcpr pref 1 iprsfrq 25 ! set-up MC barostat at 1 atm, move attempt / 25 steps ! Run variable timestep Leapfrog w/ Andersen heatbath and error tolerance of 2e-3 ! Run dynamics in periodic box dynamics leap start timestep 0.002 - nstep @nsteps nprint @nwrite iprfrq @nwrite isvfrq @nsteps iunwri 20 - firstt 298 finalt 298 - ichecw 0 ihtfrq 0 ieqfrq 0 - iasors 1 iasvel 1 iscvel 0 - ilbfrq 0 inbfrq -1 imgfrq -1 @echeck bycb - eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 ntrfq @nsteps - !PME omm andersen colfrq 250 variable vtol 3e-3 - ! turn on openmm, set-up variable - ! timestep Andersen dynamics mcpr pref 1 iprsfrq 25 ! set-up MC barostat at 1 atm, move attempt / 25 steps !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!EXAMPLE ENERGY CALCULATIONS!!!!!!!!!!!!!!!!!!!!!!!! ! Use omm on/off/clear to set-up and carry-out energy calculations using CPU and/or GPU ! Energy calculation for periodic system use PME on CPU energy eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 ! Same calculation using GPU throuhg CHARMM/OpenMM interface energy eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 - omm !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!EXAMPLE II!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! Energy calculation for periodic system use PME on CPU energy eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 omm on ! subsequent invocations of energy will use CHARMM/OpenMM interface ! Same calculation using GPU through CHARMM/OpenMM interface energy eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 omm off ! turn off use of GPU calculation but leave OpenMM "Context" intact ! Energy calculation for periodic system use PME on CPU energy eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa @kappa pme order 4 fftx 64 ffty 64 fftz 64 omm clear ! Deactivate (until next omm on) calculations using GPU !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!TEST CASES!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! The relevant test cases for the CHARMM/OpenMM functionality are: Test case Purpose c37test/ omm_acetate.inp Test whether CHARMM/OpenMM handles nbfixes correctly w/ periodic bcs. omm_dynam-vts.inp Test CHARMM/OpenMM dynamics with various integrators and variable timestep integration omm_dynamics.inp Test CHARMM/OpenMM dynamics with various integrators omm_exception.inp Test whether CHARMM/OpenMM handles nbfixes correctly w/ periodic bcs omm_modpsf.inp Test whether CHARMM/OpenMM senses psf changes and rebuilds OpenMM context omm_nbexcl.inp Test whether CHARMM/OpenMM handles nb exclusions correctly omm_nbfix.inp Test whether CHARMM/OpenMM handles nbfixes correctly omm_nonperiodic.inp Test and compare CHARMM and CHARMM/OpenMM energy and forces for vacuum system omm_periodic.inp Test and compare CHARMM and CHARMM/OpenMM energy and forces for solvated system omm_restraints.inp Test restraint methods between CHARMM and CHARMM/OpenMM for vacuum system c38test/ omm_block-periodic.inp Test BLOCK commands as implemented in CHARMM/OpenMM interface omm_block-periodic2.inp Second test of BLOCK commands as implemented in CHARMM/OpenMM interface omm_block1.inp Test of basic BLOCK commands as implemented in CHARMM/OpenMM interface omm_fixed.inp Test implementation of fixed atoms in CHARMM/OpenMM interface omm_go-model.inp Test Karanicolas/Brooks ETEN Go model w/o & w/ periodicity omm_switch-nbfix.inp Test switch/shift w/ NBFixes functioanlity of CHARMM/OpenMM interface omm_switch.inp Test switch/shift functioanlity of CHARMM/OpenMM interface omm_switch14.inp Test switch/shift functioanlity of CHARMM/OpenMM interface omm_switchpair.inp Test switch/shift functioanlity of CHARMM/OpenMM interface c39test/ omm_block_ti.inp Test BLOCK-based TI calculations through CHARMM/OpenMM interface omm_dynamics_baro2.inp Test anisotropic Monte Carlo based barostat plugin omm_resdtest.inp Test CONS RESDistance restraint implmentation through CHARMM/OpenMM omm_consdihetest.inp Test CONS DIHEdral restraint implementation through CHARMM/OpenMM