AW: The structure files for the second turn of simulation

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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