From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Aug 28 2012 - 02:10:17 CDT
Hi,
you will always need the psf file, as all of the atom, bond, angle,
dihedral... properties are defined there. So the psf is the force field
parameter file for your molecular system.
At this point namd knows everything about your system, but not the positions
of the atoms in the box. So you need also information about the coordinates
of the atoms. This is the pdb file for the simulation start.
Then namd will, during the simulation, write several restart files. One for
the changed coordinates *.coor one for the velocities *.vel (when there is
temperature, so not during minimization) and one for the box size (during
constant pressure = variable volume) *.xsc
So the following simulations will of course still need the force field
information about your molecular system, but also needs to use the updated
coordinates of the previous run, as the atoms moved already and possibly you
want to also restart with the latest atom velocities and a possibly updated
box dimension. So you will use the coor file instead of the pdb and
additionally if you already introduced temperature:
velocities whatever.vel
and if you used variable volume:
extendedsystem whatever.xsc
Good luck
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von yp sun
Gesendet: Montag, 27. August 2012 03:30
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: The structure files for the second turn of simulation
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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