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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


Thanks & Regards
Manish Kesherwani

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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.


Rick Venable
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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


output is

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; 07/02/13 04:22 PM.
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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


These are very odd and puzzling.


Rick Venable
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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.

Thanks & Regards
Manish Kesherwani

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I'm afraid I don't know much more than what is contained in openmm.doc


Rick Venable
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And what is the error you get?
Posting actual input and output (brief and relevant) is highly recommended.


Lennart Nilsson
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Thanks for repling sir

I used this input code for run dynamics and three attached file first input equilibrated structure file second output pdb and third log file

Please suggest me what is wrong in input file for run in openmm -GPU code.

Input file:


CRYSTAL DEFINE @XTLtype @A @B @C @alpha @beta @gamma
CRYSTAL READ UNIT 10 CARD

!Image centering by residue
IMAGE BYSEG XCEN 0 YCEN 0 ZCEN 0 select (segid PROA .or. segid PROB .or. segid HETA) end
IMAGE BYRESID XCEN 0 YCEN 0 ZCEN 0 sele resname TIP3 end
IMAGE BYRESID XCEN 0 YCEN 0 ZCEN 0 sele ( segid @posid .or. segid @negid ) end
set cutoff = 11
set ctofnb = 9
set ctonnb = 9
calc cutim = @cutoff
set kappa = 0.32

faster on
nbonds eps 1.0 cutnb @cutoff cutim @cutim -
ctofnb @ctofnb ctonnb @ctonnb vswi -
ewald kappa @kappa pme order 4 fftx @fftx ffty @ffty fftz @fftz

shake fast bonh tol 1.0e-5 para

set echeck = echeck -1
set nsteps = 1000
open write unit 12 card name step5.1_production.rst
open write unit 13 file name step5.1_production.dcd
! Run dynamics in periodic box
dynamics leap start timestep 0.002 -
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 @kappa pme order 4 fftx @fftx ffty @ffty fftz @fftz ntrfq @nsteps - !PME
omm langevin gamma 10 prmc iprssfrq 25 pref 1


Thanks & Regards
Manish Kesherwani

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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
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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.

Please give some suggestions

Here is input command and attached output file.

dynamics leap start timestep 0.002 -
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 @kappa pme order 4 fftx @fftx ffty @ffty fftz @fftz ntrfq @nsteps - !PME
omm langevin gamma 10 prmc iprssfrq 25 pref 1

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