[gmx-users] generation of a box of water

[Robert Johnson]

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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