Edge Water in PBC

From: Cetin Baloglu (cetinb_at_su.sabanciuniv.edu)
Date: Wed Nov 03 2004 - 05:01:40 CST


I am running a protein dynamics with namd using PB conditions, when checking
the first equilibration trajectory , I observe water molecules at the edges
leaving the box. Water molecules leaving the box something expected, but
removal of a portion at whole is something weird I guess , although my protein
moves the opposite side of the box.

I am also having a coor file problem, vmd does not open it, but namd accepts
same coor files as input. vmd says

Inconsistent atom count in file 'lyz_300.coor'.
ERROR) Could not read file lyz_300.coor

I have used different molecules and combinations for test, even coor files
produced after namd tutorials failed to open.

Here below is my config file, also picture of my protein with strange? water
movement is

I will also be glad if you comment on this conf. file .

Thanks for advance.
Cetin Baloglu

set TEMP 305
coordinates lyz_305.coor
structure lysozyme.psf
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
outputname lyz_305_eq
binaryoutput no
DCDfile lyz_305_eq.dcd
DCDfreq 1000
outputEnergies 1000
outputMomenta 0
outputPressure 0
outputTiming 0
numsteps 1
timestep 2.0
rigidBonds all
useFlexibleCell no
useConstantArea no
LangevinPiston off
stepspercycle 20
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5
cellBasisVector1 48.0, 0, 0
cellBasisVector2 0 , 45.0, 0
cellBasisVector3 0 , 0, 54.0
cellOrigin 0.73 22.08 19.69
wrapWater on
PME on
PMEGridSizeX 48
PMEGridSizeY 45
PMEGridSizeZ 55
useGroupPressure yes
exclude scaled1-4
temperature $TEMP
1-4scaling 1.0
seed 12345
langevin off
langevinHydrogen off
rescaleFreq 10000
rescaleTemp $TEMP
run 250000

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