[gmx-users] generation of a box of water

[K.F. Austen]

Hi,

Thank you for the suggestion. The difficulty is that I want to have a box 
with a higher than average density, and gromacs seems to have problems with 
this. I have tried the genbox -cs -o water.pdb -box <x> <y> <z> command and 
have tried -nmol and -maxsol, but i can't get it to give me a dense enough 
water box. Does anyone have a suggestion for getting around this? I want to 
have a density of one molecule per 28 Angs^3.

Thanks,

Kat


I think you are getting that error about NaN because you have water
molecules that are almost exactly on top of one another.

If you just want a box of water, the easiest way to do it is this:

genbox -cs -o water.pdb -box <x> <y> <z>

Here, x y and z are the box dimensions in nanometers. You can play
with the box dimensions to get close to the desired number of waters.

Bob

On 24 Jan 2007 08:19:36 +0000, K.F. Austen <kfa20 at cam.ac.uk> wrote:
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

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