constant temprature for vacuum condition in namd file

From: soroush ziaei (
Date: Fri Oct 19 2018 - 14:19:53 CDT

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:

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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:27 CST