From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Thu Apr 28 2016 - 15:00:57 CDT
Hi Olga,
You should have the same temperature control mechanism throughout the production simulations. So, if you maintain constant temperature using Langevin thermostat, you have to have the langevin thermostat lines in all your NAMD configure files.
langevinPiston part should be there as long as you want to run NPT (constant P - pressure) rather than NVP (constant V - volume).
Also, make sure you use "commotion yes", otherwise NAMD will subtract the average velocity of the system when you restart your simulations.
Maxim
> On Apr 28, 2016, at 14:49, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>
> 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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