From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Mon Jul 30 2007 - 02:27:49 CDT
Hi Folks,
I am trying to do an MD simulation for a simple test example using
ubiquitin. I first do an energy minimization, followed by heating to 300K.
After this, when I try to do an equilibration run, I get the error:
FATAL ERROR: Unable to open extended system file.
My equilibration config file looks like this:
######################TOSET############################
# molecular system
set MOL 1UBQ_PandS_wb
structure ${MOL}.psf
# after heating.
set inprot ${MOL}_heat
coordinates ${inprot}.coor
velocities ${inprot}.vel
extendedSystem ${inprot}.xsc
set temperature 300 ;# the temperature
set outputname ${MOL}_eq
set eq_restart ${MOL}_eq_restart
firsttimestep 0 ;# reset to 0 for equilibration run.
fixedAtoms off
# force field
paratypecharmm on
parameters ../topology_files/toppar/par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0
cellBasisVector1 72.165 0.0 0.0
cellBasisVector2 0.0 74.867 0.0
cellBasisVector3 0.0 0.0 77.663
cellOrigin 30.5597000122 30.3731307983 17.1436786652
wrapAll on
PME on
PMEGridSizeX 75 # size along cellBasisVector1.
PMEGridSizeY 75 # along cellBasisVector2.
PMEGridSizeZ 80
# use numbers with small integer factors: 2,3,5.
# approximations
switching on
switchdist 10
cutoff 12
pairlistdist 13.5
# center-of-mass motion is automatically removed.
# integrator
timestep 1.0 ;# in fs.
stepspercycle 20 ;# default
nonbondedFreq 2 ;# same as BerendsenPressureFreq
fullElectFrequency 2
# output
outputName $outputname
dcdfreq 1000 ;# every ps
xstFreq 1000
outputEnergies 1000
outputPressure 1000
outputtiming 1000
binaryoutput no
# for restarting:
restartname $eq_restart
restartfreq 10000
restartsave yes
binaryrestart no ;# yes will preserves more accuracy.
# Temperature coupling via Langevin dynamics.
langevin on
langevinTemp $temperature
langevinDamping 1.0 ;# from mailing-list
langevinHydrogen on
# Pressure coupling by Nose-Hoover Langevin piston pressure control
LangevinPiston on
LangevinPistonTarget 1.01325 ;# in bar.
LangevinPistonPeriod 200 ;# in fs.
LangevinPistonDecay 100
LangevinPistonTemp $temperature ;# set same as langevinTemp.
# GPressure seems to fluctuate about 1.0, betw -2K to 2K.
useGroupPressure yes # use hydrogen-group based virial. use with rigidBonds.
# GROMACS: ref_p = 1.0 bar; compressibility = 4.5e-5 bar-1; tau_p = 0.5 ps
# but tau_p = 0.1ps gave errors.
margin 3.0 ; # increase margin to overcome problem with
decreasing cell size.
# to use SHAKE to constraint all bonds during free MD only.
rigidBonds all
# short equilibration run
run 50000 ; # 50 ps
Has anyone come across this error before. Or can anyone spot some obvious
problem with my configuration file?
Thanks,
Arun
-- *********************************************** Arun Krishnan, Ph.D, Assistant Professor, Institute for Advanced Biosciences, Keio University, Center Building, Tsuruoka, Yamagata 997-0035 Japan Phone: +81 (0)235-29-0824 Email: krishnan_at_ttck.keio.ac.jp URL: http://www.iab.keio.ac.jp/~krishnan **********************************************
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:01 CST