From: yp sun (sunyeping_at_yahoo.com.cn)
Date: Sun Aug 26 2012 - 20:30:04 CDT
Dir Sir,
When we run the real NAMD, we usually should do several turns of pre-balance. In the first turn of prebalance, we use psf file as the structure file. But in the second turn of simulation, I am not sure if we should use the coor file generated in the first turn to replace the psf file as the structure file. I do this in my NAMD but got the error message: FATAL ERROR: UNABLE TO FIND "PSF" STRING IN PSF FILE RI-10_eq1_o.coor. Could you tell me what does it mean? The content of my conf file RI-10_wb_ionized_eq2.conf is as following:
structure RI-10_eq1_o.coor
coordinates RI-10_wb_ionized.pdb
set temperature 310
set outputname RI-10_eq2_o
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 86.6409 0.0 0.0
cellBasisVector2 0.0 77.0141 0.0
cellBasisVector3 0.0 0 75.0888
cellOrigin 31.625 -36.5377 -3.52252
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
#manual grid definition
#PMEGridSizeX 96
#PMEGridSizeY 81
#PMEGridSizeZ 80
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
#Harmonic constrain
if {0} {
constraints on
consref RI-10_wb_ionized_constr.pdb
conskfile RI-10_wb_ionized_constr.pdb
conskcol B
constraintscaling 10.0
}
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 1000
Could you tell me what leads to the error?
Best Regards!
Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
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