Dear Sir, I am using GPU-OpenMM interaface for running dynamics in GPU. Protein is out of box in properly equilibrated solvated box when i performing MD run . Please suggest me why protein is coming out of box only when i use openmm . in normal MD there is no centering problem occured.
Below i am writing MD code whic i used in Openmm-gpu run.
!Image centering by residue IMAGE BYSEG XCEN @xcen YCEN @ycen ZCEN @zcen select (segid PROA .or. segid PROB .or. segid HETA) end IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele resname TIP3 end IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele ( segid @posid .or. segid @negid ) end ! Nonbonded Options 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 !nbonds atom vatom vfswitch bycb - ! ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 - ! inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 - ! ewald pmew fftx @fftx ffty @ffty fftz @fftz kappa .34 spline order 6 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 !use a restraint to place center of mass of the molecules near the origin MMFP GEO rcm sphere - Xref @xcen Yref @ycen Zref @zcen XDIR 1.0 YDIR 1.0 ZDIR 1.0 - harmonic FORCE 10.0 select .not. ( hydrogen .or. resname TIP3 .or. segid @posid .or. segid @negid ) end END cons harm force 8 exponent 3 select hydrogen end coor translate xdir 1.3 select all end set nsteps = 1000 open write unit 12 card name step5.1_production.rst open write unit 13 file name step5.1_production.dcd set echeck = echeck -1 dynamics leap start timestep 0.001 - nstep @nsteps nprint 100 iprfrq 1000 - firstt 300 finalt 300 twindl -5.0 twindh 5.0 - ichecw 0 teminc 30.0 ihtfrq 0 ieqfrq 0 - iasors 1 iasvel 1 iscvel 0 - ilbfrq 0 inbfrq -1 imgfrq -1 @echeck - iunread -1 iunwri 12 iuncrd 13 - eps 1.0 cutnb @cutoff cutim @cutim ctofnb @ctofnb ctonnb @ctonnb vswi - ewald kappa .34 pme order 6 fftx @fftx ffty @ffty fftz @fftz ntrfq @nsteps - omm langevin gamma 5.0 - prmc pref 1 iprsfrq 25
It may depend on the values used for @xcen, etc. for the MMFP restraint; I suggest trying w/o restraints and then find the protein center. I found that OpenMM in CHARMM seems to shift the Cartesian coordinates such that the minimum corner of the unit cell is at the origin, instead of the origin being the center. Also, since the OpenMM interface is still somewhat developmental, it's not clear if all of the restraints in CHARMM are fully supported; the documentation does not address the issue.
Thanks sir for suggestion. i checked without MMFP restraint on protein Results are same protein is out of solvated box. How to solve this problem please give suggestion
I also xcen=0 is giving in image centering
DCNTRL> Langevin integration requested. DCNTRL> OpenMM interface requested for energy and dynamics calculations. DCNTRL> Constant temperature w/ OpenMM using Langevin heatbath requested. DCNTRL> Reference heatbath temperature is 300.000K DCNTRL> Using friction coefficient value of 10.000 ps^-1 DCNTRL> CPT dynamics through OpenMM interface requested using Langevin heatbath. DCNTRL> MC barostat coupled to reference pressure 1.00 atmospheres. DCNTRL> MC barostat using reference temperature 300.00 K. DCNTRL> MC barostat volume move attempted every 25 timesteps. NSTEP = 1000 NSAVC = 10 NSAVV = 10 ISCALE = 0 ISCVEL = 0 IASORS = 1 IASVEL = 1 ICHECW = 0 NTRFRQ = 1000 IHTFRQ = 0 IEQFRQ = 0 NPRINT = 100 INBFRQ = -1 IHBFRQ = 0 IPRFRQ = 1000 ILBFRQ = 0 IMGFRQ = -1 ISVFRQ = 0 NCYCLE = 1000 NSNOS = 10 FIRSTT = 300.000 TEMINC = 30.000 TSTRUC = -999.000 FINALT = 300.000 TWINDH = 5.000 TWINDL = -5.000
TIME STEP = 4.09097E-02 AKMA 2.00000E-03 PS
RANDOM NUM. GEN. SEED(S) = 1151852549 1151852549 1151852549 1151852549
SHAKE TOLERANCE = 0.10000E-04 NUMBER OF DEGREES OF FREEDOM = 61928
GAUSSIAN OPTION IS 1 VELOCITIES ASSIGNED AT TEMPERATURE = 375.0000 SEED FOR RANDOM NUMBER GENERATOR IS: SEEDS> 1151852549 1151852549 1151852549 1151852549
DETAILS ABOUT CENTRE OF MASS POSITION : -0.11498689 1.58487956E-02 -0.12708586 VELOCITY : -2.55257175E-03 2.51749404E-03 -1.34131645E-03 ANGULAR MOMENTUM : 3326.1685 3772.3654 9957.1191 KINETIC ENERGY : 1.3681834 Initializing OpenMM context OpenMM version 5.0 Specifying OpenMM Ewald error tolerance 1.911E-04 OpenMM will use KAPPA of 3.117E-01 A^(-1) OpenMM nodes in PME mesh will be closest product of 2, 3 and 5 to 80 80 80 Using OpenMM platform OpenCL OpenCLPlatformIndex = 0 OpenCLPrecision = single OpenCLDeviceIndex = 0
Thanks & Regards Manish Kesherwani
Last edited by Manish Kesherwan; 07/02/1304:22 PM.
Sorry, but the output you've posted doesn't tell me anything new about the problem, and doesn't confirm the lack of restraints. I don't have a lot of OpenMM experience myself, and have not observed the problem you seem to be having.
Besides the modified cutoffs and reduced SHAKE tolerance (usually bad ideas), I noticed these curious commands in the original input--
cons harm force 8 exponent 3 select hydrogen end coor translate xdir 1.3 select all end
sorry sir i deleted these two commands after that also there is no changes problems are remained. I also didn't get these problem in normal CPU run. it may be box decomposition in memory allocation for GPU and unable to assign interaction between segment of system. I have C37b2 version of charmm.
Please can you suggest some charmm-openmm interface developer or some sample script.
Well, I don't know what to say. You are apparently trying to run before you can crawl. There is a specific error message in your output file, which is unrelated to GPU-usage and water centering, as far as I can tell. Since you use CHARMM-GUI, I think your best option is to ask for support from the CHARMM-GUI people (I am not familiar with the peculiarities of CHARMM-GUI).
Lennart Nilsson Karolinska Institutet Stockholm, Sweden
Sorry sir i corrected that error in command now it's script are running in GPU but still output structure is not centering.
sir i modified totally script according to run in GPU. i removed MMFF contraint and nonbonded parametr from script. so it's changed from charmmgui given script. i don't know how to center the molecule.
Sir i tried with energy command along with omm then it's giving mmff contribution of energy . but i faced one problem that protein molecule is not coming in center of box during simulation but afer generating trajactory we can align frames with protein molecule then molecule will be in centre. If you have some other solution regarding centering of protein molecule in waterbox please sugggest me. Did you tried simulation with openmm. how was your trajactory.
"It may depend on the values used for @xcen, etc. for the MMFP restraint; I suggest trying w/o restraints and then find the protein center. I found that OpenMM in CHARMM seems to shift the Cartesian coordinates such that the minimum corner of the unit cell is at the origin, instead of the origin being the center. Also, since the OpenMM interface is still somewhat developmental, it's not clear if all of the restraints in CHARMM are fully supported; the documentation does not address the issue."
I am running equilibration dynamics in membrane protein using NVIDIA TESLA GPU card(openmm -charmm). when i am using multigpu(more than one gpu) then energy drift is too high around( 1000000 Kcal). Can u specify how we can rectify this.
Since the questions and answers in this post mostly involve the OpenMM interface, it was moved here to this forum.
The energy drift is a function of the numerical precision, and has been shown to be fairly bad when using a GPU with single precision. Mixed precision can improve that somewhat, and double precision is better, but costs more, in terms of time to completion. The env var OPENMM_PRECISION can be used to control the precision.
The default prmc code does not implement an anisotropic pressure tensor, is therefore not appropriate for simulating membrane bilayer based systems. Code has been under development for this, but it does not appear to be in any of the public beta release versions of OpenMM/CHARMM.
My system is a small peptide system (12 AA's) so I doubt size is the issue. When run on CPUs, the peptide is nicely centred in the water box. Commenting out the block means the simulation runs using OpenMM acceleration but the peptide flaps around outside the centred water box.