molecule leaves water box during md

From: Irene Newhouse (einew_at_hotmail.com)
Date: Thu Jul 19 2007 - 13:38:02 CDT

I minimized my molecule. No problems. I did an equilibration at constant P. No problems. I tried to do MD at constant V, using the volume that pertained at the end of the P-equilibration. The molecule did not stay centered in the cell, and by 3ns, it had moved completely outside the waters, which still formed a nice coherent box.

Can someone please tell me what I'm doing wrong?

This is the control/config file for the md:

# input system......
structure lstawi.psf
coordinates lstawir_p.coor

#..force field........................
paratypecharmm on
parameters par_kitsink.prm
exclude scaled1-4
1-4scaling 1.0
dielectric 1.0

switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 20
rigidBonds all
rigidTolerance 0.00001
rigidIterations 100

# Ewald EL..........................
PME on
PMETolerance 0.000001
PMEGridSizeX 27
PMEGridSizeY 40
PMEGridSizeZ 27

#integrator ............
timestep 1.0
fullElectFrequency 4

#output....................
outputenergies 10000
outputtiming 10000
binaryoutput no
outputname lstawi_md
restartname lstawir_md
restartfreq 10000
binaryrestart no
DCDfile lstawi_md.dcd
dcdfreq 10000

#MD protocol..............
seed 3010
numsteps 20000000
temperature 310

# periodic boundary conditions......
cellBasisVector1 29.9 0.0 0.0
cellBasisVector2 0.0 41.758 0.0
cellBasisVector3 0.0 0.0 29.313
cellOrigin -2.3 8.5 -1.565

wrapWater on

Thanks ever so much!
Irene Newhouse
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