FEP simulation: protein moving out of water box.

From: venkata agasthya (kvagasthya_at_gmail.com)
Date: Tue Nov 05 2013 - 19:39:51 CST

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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.

• Next message: Niklaus Johner: "Re: FEP simulation: protein moving out of water box."
• Previous message: Francesco Pietra: "Re: Restarting T-REMD with colvars"
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