Problem with temperature increase in equilibration.

From: Diego Alejandro Vargas (vardiego9_at_gmail.com)
Date: Thu Oct 30 2008 - 11:14:54 CDT

Hello,
I am trying to run a minimization and equilibration simulation for fascin
using a linux amd 64 cluster with Rocks operating system. The simulation is
failing after the minimization steps (5000). I am trying to gradually
increase the temperature from 0 to 310K before equilibration, but I am
encountering the following problems:

>From the discussion board I tried using the following code:

reassignFreq 500
for { set i 0 }{$i < 310 }{incr i 10 }{
reassignTemp $i
run 500
}

But the simulation fails with:

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 5000
WRITING COORDINATES TO DCD FILE AT STEP 5000
WRITING COORDINATES TO RESTART FILE AT STEP 5000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 5000
FINISHED WRITING RESTART VELOCITIES
TCL: Setting parameter reassignFreq to 500
FATAL ERROR: Setting parameter reassignFreq from script failed!

I am adding my configuration file at the end of this message in case it may
be of help.

Thank you for your attention,
Diego A. Vargas
_______________________________________________________________

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure
/home/Diego/Diego/NAMD_2.6_Linux-amd64/fascin_structures/ser39ala/ser39ala_wb.psf
coordinates
/home/Diego/Diego/NAMD_2.6_Linux-amd64/fascin_structures/ser39ala/ser39ala_wb.pdb

set temperature 310
set outputname
/home/Diego/Diego/NAMD_2.6_Linux-amd64/fascin_structures/ser39ala/ser39ala_wb_eq

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters
/home/Diego/Diego/NAMD_2.6_Linux-amd64/fascin_structures/common/par_all27_prot_lipid.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellBasisVector1 48. 0. 0.
cellBasisVector2 0. 58. 0.
cellBasisVector3 0. 0 46.
cellOrigin 62. 89. 10.

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 50
PMEGridSizeY 50
PMEGridSizeZ 50

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
minimize 5000

# Gradual Temperature increase
reassignFreq 500
for { set i 0 }{$i < 310 }{incr i 10 }{
reassignTemp $i
run 500
}

run 250000 ;# 500ps

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