Re: restarting files converge to new temperature

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Wed Feb 13 2008 - 02:13:09 CST

Hi,

My configuration file looks like this

#################################
# NAMD Configuration file
#################################

# Setting path to parameter and topology files
set path ./par_all27_prot_na.prm

# set PDB and PSF file
set pdb min_sol.pdb
set psf sol_Dder.psf

# Set number of MD steps 5ns
set md 1000000

# Restarting simulation due
# to periodic cell has become
# too small
set inputname min_whole_sys

Bincoordinates $inputname.restart.coor
Binvelocities $inputname.restart.vel
ExtendedSystem $inputname.restart.xsc

#########################################################
proc get_first_ts { xscfile } {
  set fd [open $xscfile r]
  gets $fd
  gets $fd
  gets $fd line
  set ts [lindex $line 0]
  close $fd
  return $ts
}

set firstts [get_first_ts $inputname.restart.xsc]
########################################################

#################################
# Adjustable parameters
#################################

structure $psf
coordinates $pdb

outputName restart_Dder

##################################

restartfreq 500
# 500 steps = every 1ps
dcdfreq 2000
xstFreq 500

outputEnergies 100
# 100 steps - every 0.2 ps
outputTiming 1000

# Shows time per step and time to completion

firsttimestep 0

#################################
# Simulation parameters
#################################

# Input
paraTypeCharmm on

parameters $path

#temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10
# Switchdist = Cutoff - 2

# Promise that atom will not move more than 2A in a cycle
pairlistdist 14
# Cutoff + 2
stepspercycle 10
# Redo pairlists every ten steps

# Integrator Parameters
timestep 0.5
# 0.5 fs/step
rigidBonds none
# needed for 2fs steps
nonbondedFreq 1
# nonbonded forces every step
fullElectFrequency 2
# PME only every other step

wrapWater on
wrapAll on

# Particle Mesh Ewald

if {$pme == 1} {
   PME yes
   PMEGridSizeX 64
   PMEGridSizeY 64
   PMEGridSizeZ 64
}

run $md

should I include the barostat and thermostat as well in the restart-file?

####### PRES CONTROL
langevinPiston on
# Appling the langevinpiston for pressure control
langevinPistonTarget 1.01325
# One atomsheric pressure at sea level
langevinPistonPeriod 100
# barostat oscillation time scale for LP method
langevinPistonDecay 50
# barostat damping time scale for LP
LangevinPistonTemp $temperature
# barostat noise temperature for LP

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigid bonds
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, maybe for membrane
####### TEMP CONTROL
langevin on
# langevin dynamics
langevinDamping 5.
# damping coefficient of 5/ps
langevinTemp $temperature
# Random noise at this level
langevinHydrogen no
# Do not couple bath to hydrogens

should this be included as well with the $temperature commented out? Any
help or advise appreciated -
thanks in advance
Best

On Feb 12, 2008 8:34 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:

> Hi Jorgen,
> are you running with temperature control? It isn't apparent from your
> config file.
> Best,
> Peter
>
> Jorgen Simonsen wrote:
> > Hi,
> >
> > I had a crash with the MD run and would like to restart the
> > calculation. I use the restart files first with the extension *.coor,
> > *.vel, *.xsc which gave an error that it could read the *.coor. I
> > moved the files *.coor.old, *.vel.old, *.xsc.old into *.coor, *.vel,
> > *.xsc and restarted the calculation - the problem is that instead of
> > using a temperature of 300 K it is now using a temperature of around
> > 270 K. How to resolve this and what is the problem?
> > Any help or advise appreciated - thanks in advance
> >
> > Best
> > J
> >
> > # Restarting simulation
> > set inputname min_whole_sys
> >
> > Bincoordinates $inputname.restart.coor
> > Binvelocities $inputname.restart.vel
> > ExtendedSystem $inputname.restart.xsc
> >
> > #########################################################
> > proc get_first_ts { xscfile } {
> > set fd [open $xscfile r]
> > gets $fd
> > gets $fd
> > gets $fd line
> > set ts [lindex $line 0]
> > close $fd
> > return $ts
> > }
> >
> > set firstts [get_first_ts $inputname.restart.xsc]
> >
>

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