From: Bruno Luís Pinto de Oliveira (boliveira_at_itn.pt)
Date: Sat Nov 26 2011 - 10:15:13 CST
Dear NAMD users,
I would like to ask for your help in how to restart a FEP simulation.
I found some related post in the forum but I still have some doubts.
My calculation terminated almost at the end (lambda = 0.01).
At lambda = 0.01 the net change is 28.58 kcal/mol. I did the restart at lambda = 0.1, however I found some problems in the overall dG calculation.
After the first 120k steps the calculated net change is 3.29 kcal/mol instead of a value close to 28.58 kcal/mol.
I am guessing that the restart at some point should give the same energy as before it aborted. Am I right?
Below I attached my config file (my outputs have the name back.xxx).
Can someone help me find what I'm doing wrong, please? Thanks in advance!
Regards
Bruno
###################################################
# ALCHEMICAL TRANSFORMATION
###################################################
# INPUT
parameters MOL_par_all27_ISM.prm
paraTypeCharmm on
exclude scaled1-4
1-4scaling 1.0
# TOPOLOGY
structure solvated.psf
# COORDINATES
coordinates solvated.pdb (here I am not sure if I should use back.coor.old or solvated.pdb???!!!!!!!)
bincoordinates back.coor
# VELOCITIES
#velocities alchemy_0.vel
binvelocities back.vel
# CELL
extendedSystem back.xsc
# OUTPUT FREQUENCIES
outputenergies 1000
outputtiming 1000
outputpressure 1000
restartfreq 1000
XSTFreq 1000
dcdfreq 1000
# OUTPUT AND RESTART
outputname back_rest_0
restartname back_rest
binaryoutput no
binaryrestart yes
# PME
PME yes
PMETolerance 10e-6
PMEInterpOrder 4
PMEGridSizeX 71
PMEGridSizeY 55
PMEGridSizeZ 71
cellOrigin -53.7 131.5 -16.6
# WRAP WATER FOR OUTPUT
wrapAll on
# CONSTANT-T
langevin on
langevinTemp 310.0
langevinDamping 5.0
# CONSTANT-P
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 50
LangevinPistonTemp 310
useGroupPressure yes
useflexiblecell no
# SPACE PARTITIONING
splitpatch hydrogen
hgroupcutoff 2.8
stepspercycle 10
margin 2.5
# CUT-OFFS
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 16.0
# RESPA PROPAGATOR
timestep 1.0
fullElectFrequency 2
nonbondedFreq 1
# SHAKE
rigidbonds all
rigidtolerance 0.00000001
rigiditerations 400
# COM
commotion no
# FEP
source fep.tcl
alch on
alchType fep
alchFile solvated.fep
alchCol B
alchOutFile back_rest.fepout
alchOutFreq 1
alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdwShiftCoeff 5.0
alchDecouple yes
# LOOP OVER LAMBDA-STATES
alchEquilSteps 16000
set nSteps 120000
set dLambda 0.05
#set init {1.0 0.9999999 0.999999 0.99999 0.9999 0.999 0.99 0.95 0.9}
set end {0.05 0.01 0.001 0.0001 0.00001 0.000001 0.0000001 0.0}
#runFEPlist $init $nSteps
runFEP 0.1 0.05 $dLambda $nSteps
runFEPlist $end $nSteps
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