From: soroush ziaei (soroush.ziaei7337_at_gmail.com)
Date: Fri Oct 19 2018 - 14:19:53 CDT
hi.
i dealt with an error in terminal about constant temperature for fep
simulation in vaccum, that says; Alchemical FEP can be performed only in
constant temperature simulations.
i puted the last config file (equilibrium) below:
#2.namd
numsteps 15000
structure fu.psf
coordinates fu.pdb
outputName eq2
XSTfile eq2.xst
bincoordinates eq1.coor
binvelocities eq1.vel
extendedSystem eq1.xsc
langevin off
langevinDamping 3
langevinTemp 310
langevinHydrogen on
switching on
switchDist 10
cutoff 12
pairlistdist 14
margin 3
binaryOutput yes
binaryRestart yes
parameters par file.par
parameters par2.prm
paraTypeCharmm on
wrapAll yes
wrapNearest yes
COMmotion no
outputEnergies 500
outputTiming 500
xstFreq 500
dcdFreq 250
restartFreq 500
timestep 1
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20
Pme off
PmeGridSizeX 40
PmeGridSizeY 40
PmeGridSizeZ 40
exclude scaled1-4
1-4scaling 1
alch on
alchType FEP
alchFile fu.fep
alchCol B
alchOutFile forward-off.fepout
alchOutFreq 5
set numSteps 500
alchDecouple off
set Lambda0 0.0
set dLambda 0.1
while {$Lambda0 <= 1.0} {
alchLambda $Lambda0
set Lambda0 [expr \$Lambda0 + \$dLambda]
alchLambda2 $Lambda0
run 10000
}
what's wrong with this part of config file to perform vacuum condition?
regards, soroush
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