From: Ahlam Al-Rawi (ahlamumali_at_gmail.com)
Date: Wed Aug 22 2007 - 19:49:12 CDT
Dear User,
I am running MD simulations of a system of protein channel in POPC. Due to
the large size of my system and limited computer resources , I had to
cut my simulations into several runs.
After running the system for the third run I got this error:
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1384000
FATAL ERROR: Error on renaming file final-3.restart.xsc to
final-3.restart.xsc.old: No such file or directory
This is the conf file that I use
Your help is always great!!!
Thanks
Ahlam
....
forcefield
paratypecharmm on
parameters par_all27_prot_lipid-a.prm
#molecules
structure ionized.psf
coordinates ionized.pdb
Bincoordinates final-2.restart.coor
Binvelocities final-2.restart.vel
ExtendedSystem final-2.restart.xsc
#...................
# continuing a run
#
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 final-2.restart.xsc]
firsttimestep $firstts ;# last step of previous run
numsteps 201000 ;# run stops when this step is reached
#....................
#temperature 310
#temp & pressure coupling
langevin on
langevinTemp 310
langevinDamping 1
useGroupPressure yes
useFlexibleCell yes
LangevinPiston on
LangevinPistonTarget 1
LangevinPistonPeriod 100
LangevinPistonDecay 50
LangevinPistonTemp 310
#output
outputname final-3
outputEnergies 10
restartfreq 500
DCDfreq 500
binaryoutput no
binaryrestart yes
outputTiming 100
wrapAll on
wrapNearest on
#integrator
timestep 1
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
#approximations
rigidBonds off
rigidTolerance 0.000001
cutoff 12
switching on
switchdist 10
pairlistdist 14
exclude scaled1-4
1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber
PME on
#PMEGriDSPACING 1.0
PMEGridSizeX 100
PMEGridSizeY 100
PMEGridSizeZ 100
run 201000
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