[gmx-users] generation of a box of water

[K.F. Austen]

Hi,

I am trying to generate a box of purely water molecules (101 molecules) 
using the following commands:

/usr/local/gromacs/bin/genbox -cp box.pdb -ci spc216 -o water.pdb -nmol 101

(I've also tried using tip5p but have the same problem.)

box.pdb looks like this:

TITLE     NOTHING
REMARK    THIS IS A SIMULATION BOX
CRYST1    9.7404  14.9488  20.0870 90.00  90.00  90.00 P 1           1
MODEL        1
TER
ENDMDL

The box that is generated has too many close contacts... Even after energy 
minimization, there are atoms too close together. I've played around with 
-seed, varying between 20 and 2050 but whatever value I use, the system 
will not minimise to a sensible enough configuration (ie: forces 1003 or 
more).

The .mdp file looks like this:

; VARIOUS PREPROCESSING OPTIONS =
title                    =
cpp                      = /lib/cpp
include                  =
define                   = -DFLEXIBLE

; RUN CONTROL PARAMETERS =
integrator               = l-bfgs
; start time and timestep in ps =
tinit                    = 0
dt                       = 0.001
nsteps                   = 100
rlist                    = 0.4
rcoulomb                 = 0.4
rvdw                     = 0.4

; ENERGY MINIMIZATION OPTIONS =
emtol                    = 0.00001
emstep                   = 0.1
nstcgsteep               = 1000

I've used steep and l-bfgs, the latter of which seems to be slightly more 
effective but even so if I try to run an MD on the system from the 
configuration I get this error:

Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 280 ]
Please report this to the mailing list (gmx-users at gromacs.org)


NB: We are using V 3.3.1 of gromacs.

Please help!

Kat