MM works MD does not in Fixed system

From: Pedro Borkowski (pedro.borkowski_at_gmail.com)
Date: Fri Mar 30 2007 - 15:45:42 CDT

Hey all, I want to do a minimization with molecular mechanics (MM)
then a molecular dynamic (MD) simulation of a system which includes
fixed positioned collagen peptides and water.

So the collagen peptides are fixed and the water are not.

But after running the simulations repeatedly, most of the simulations
worked through the MM but didnot begin the MD simulations. Other
worked through the MM but some of the MD.

I don't know what im doin wrong. but i know the problem has to do
with the fixed positioned peptides because i ran simulations much
larger than this and the simulations worked.

So this is the NAMD configuration file Please have a look

#############################################################
## JOB DESCRIPTION ##
#############################################################

# Simulation to fill the gaps between the EKG models of collagen

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure sol.psf
coordinates sol.pdb

#binCoordinates dsol.restart.coor
#binVelocities dsol.restart.vel
#extendedSystem dsol.restart.sxc

set temperature 277
set outputname dsol

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters par_all27_prot_na_hyp.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# 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 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellBasisVector1 125. 0. 0.
cellBasisVector2 0. 192. 0.
cellBasisVector3 0. 0. 40.
cellOrigin 12.2 6.2 22.8

wrapAll on

# PME (for full-system periodic electrostatics)
# Should be equal to the Basis Vectors
PME yes
PMEGridSizeX 126
PMEGridSizeY 192
PMEGridSizeZ 40

margin 2.5

# 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.
langevinPistonDecay 50.
langevinPistonTemp $temperature

# Fixed Atoms Constraint (set PDB beta-column to 1)
fixedAtoms on
fixedAtomsFile fixed_crystal_sol.pdb
fixedAtomsCol B

# Output
outputName $outputname

outputTiming 500
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100

#############################################################
## EXTRA PARAMETERS ##
#############################################################

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
minimize 50000
reinitvels $temperature
run 15000

-- 
-Pedro Borkowski

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