From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu Apr 28 2016 - 14:49:45 CDT
Hi all,
just a quick question, do I understand it correctly that langevin
section should not be in a restart configuration file at all? I.e. to
restart my simulation I should remove/comment out this whole section
(as opposed to only removing the langevinTemp $temperature line):
# Constant Temperature Control
langevin on
langevinDamping 1
langevinTemp $temperature
langevinHydrogen no
What about langevinPistonTemp $temperature, should that part be
commented out as well?
Thanks in advance!
Olga
P.S. Does this restart script look right?
structure ionized.psf
coordinates ionized.pdb
outputName test_1
if {1} {
set inputname test
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
extendedSystem $inputname.xsc
}
firsttimestep 26500
paraTypeCharmm on
parameters my_parameters.prm
wrapWater on #what about this option, is it needed?
wrapAll on
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
timestep 2.0 ;# 2fs/step
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
#PME
if {0} {
PME yes
PMEGridSpacing 1.0
}
if {0} {
useGroupPressure yes ;
useFlexibleCell no ;
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
}
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
run 10000000
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