From: Niklaus Johner (niki.johner_at_gmail.com)
Date: Tue Nov 05 2013 - 21:21:48 CST
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N.
On Nov 6, 2013, at 2:39 AM, venkata agasthya wrote:
> Hi,
>
> I have run an FEP calculation of a protein ligand complex for 5000000 steps. When I checked the trajectory files by loading into VMD I found that my protein complex moves out of the water box. I have tried the simulation by removing the COM motion and keeping the zero momentum but the problem still persists. Is there a way to keep the complex in the water box during the simulation?. I am also attaching my configuration file for the forward run. Please help.
>
> ###################################################
> # Estrogen Receptor:Bisphenol A
> ###################################################
>
>
> # MD SETUP
>
> timestep 2.0
> ##numsteps 5000000
>
>
> # FLEXIBLE CELL
>
> useflexiblecell no
>
>
> # INPUT
>
> structure ionized.psf
>
> parameters /work/agasthya/bpa/par_all27_prot_lipid.prm
> parameters /work/agasthya/bpa/est_bpa.prm
> paraTypeCharmm on
>
> coordinates ionized.pdb
> bincoordinates equilibration.coor
> binvelocities equilibration.vel
> extendedsystem equilibration.xsc
>
>
> # OUTPUT
>
> outputenergies 5000
> outputtiming 5000
> outputpressure 5000
> binaryoutput yes
>
> outputname forward
> restartname forward
> restartfreq 5000
> binaryrestart yes
>
> XSTFreq 5000
>
>
> # DCD
>
> DCDfreq 5000
> DCDfile forward.dcd
>
>
> # PME
>
> PME yes
> PMETolerance 10e-6
> PMEInterpOrder 4
>
> PMEGridSizeX 100
> PMEGridSizeY 100
> PMEGridSizeZ 100
>
>
> # WRAP WATER FOR OUTPUT
>
> wrapAll on
>
>
> # CONSTANT-T
>
> langevin on
> langevinTemp 300.0
> langevinDamping 1.0
>
>
> # CONSTANT-P
>
> LangevinPiston on
> LangevinPistonTarget 1
> LangevinPistonPeriod 75
> LangevinPistonDecay 25
> LangevinPistonTemp 300
> StrainRate 0.0 0.0 0.0
> useGroupPressure yes
>
>
> # SPACE PARTITIONING
>
> splitpatch hydrogen
> hgroupcutoff 2.8
> stepspercycle 10
> margin 1.0
>
>
> # CUT-OFFS
>
> switching on
> switchdist 9.0
> cutoff 10.0
> pairlistdist 11.0
> limitDist 1.3
>
>
> # RESPA
>
> fullElectFrequency 2
> nonbondedFreq 1
>
>
> # 1-4 NON-BONDED
>
> exclude scaled1-4
> 1-4scaling 1.0
>
>
> # COM
>
> commotion no
> zeromomentum on
>
>
> # SHAKE
>
> rigidbonds all
> rigidtolerance 0.000001
> rigiditerations 400
>
>
>
> # FEP PARAMETERS
>
> source /work/agasthya/bpa/fep.tcl
>
> alch on
> alchType FEP
> alchFile solvate.fep
> alchCol B
> alchOutFreq 10
> alchOutFile forward.fepout
>
> alchElecLambdaStart 0.0
> alchVdwLambdaEnd 1.0
> alchVdwShiftCoeff 5.0
> alchdecouple on
>
> alchEquilSteps 100
> set numSteps 5000000
>
> set dLambda 0.25
>
> runFEP 0.0 1.0 $dLambda $numSteps
>
> Thanks,
> Agasthya.
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