From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Thu Apr 07 2016 - 13:13:38 CDT
Dear all,
I want to heat my system from 300 K to 700 K via 50 K heating steps,
equilibrate system for a few ps and then same cooling procedure from 700K
down to 300 K with 50 K steps. My configuration file is as follows:
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Equilibration G5 OH terminate Alkyne dendron in a Water Box
# Parameters were taken from CHARMM 36
# Simulated annealing
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure Alkyne-SA/A_OH.psf
coordinates Alkyne-SA/A_OH.pdb
set temperature 298
set outputname A_OH_SA
firsttimestep 0 ;# last step of previous run
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters Alkyne-SA/par_all36_prot.prm
parameters Alkyne-SA/par_all36_Alkyne.prm
temperature $temperature
# Force-Field Parameters
exclude scaled1-4 ;# These are specified by CHARMM
1-4scaling 1.0 ;# These are specified by CHARMM
cutoff 12.0 ;# may use smaller, maybe 10.0, with PME
switching on
switchdist 10.0 ;# cutoff - 2.0
pairlistdist 14.0 ;# Promise that atom won’t move more than 2A
in a cycle, cutoff + 2
# Integrator Parameters
timestep 1.0 ;# 1.0 fs/step
rigidBonds all
nonbondedFreq 1 ;# nonbonded forces every step
fullElectFrequency 2 ;# PME only every other step
stepspercycle 10 ;# redo pairlists every ten steps
# Constant Temperature Control
langevin on ;# langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, maybe for membrane
# Output
outputName $outputname
restartfreq 500 ;# 500 steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
outputTiming 1000 ;# shows time per step and time to completion
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
#minimize 25000
#reinitvels $temperature
#simulated annealing
for { set temperature 298 } { $temperature <= 698 } { incr temperature 50 }
{
run 20000
reinitvels $temperature
langevinTemp $temperature
}
run 500000
for { set temperature 698 } { $temperature >= 298 } { incr temperature -50}
{
run 20000
reinitvels $TEMP
langevinTemp $TEMP
}
run 1000000 ; 1 ns
But I get this error message:
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 288000
PRESSURE: 288100 0 0 0 0 0 0 0 0 0
GPRESSURE: 288100 0 0 0 0 0 0 0 0 0
PRESSAVG: 288100 0 0 0 0 0 0 0 0 0
GPRESSAVG: 288100 0 0 0 0 0 0 0 0 0
ENERGY: 288100 243.0280 486.5293 172.3114
14.5636 334.2073 85.4743 0.0000
0.0000 889.1184 2225.2322 710.1980
1336.1138 2226.6211 687.6288
ERROR: Constraint failure in RATTLE algorithm for atom 6!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
====================================================
WallClock: 130.864319 CPUTime: 130.864304 Memory: 98.730469 MB
[Partition 0][Node 0] End of program
Any help will be appreciated.
Regards,
Farideh
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:59 CST