[gmx-users] RE: grompp and box size

[Tsjerk Wassenaar]

Hi,

On Fri, Aug 8, 2008 at 3:12 PM, Vitaly Chaban <chaban at univer.kharkov.ua> wrote:
> No problem, Prasun. :) Just open conf.gro and see the last string
> there. Divide the least number by 2 and type it in the  grompp.mdp as
> your new cutoff.
>

This is a good way of turning gromacs into the well-known expensive
random number generator!
Unless there's a good reason why the box has the dimensions it should
have and unless one knows what he/she's doing by changing rvdw, the
rvdw shouldn't be modified in this way. The cut-off (shift/...) is an
integral part of a force field. A force field is parameterized using
(and thus to be used with) a specific combination of simulation
parameters. Changing these at random will affect the integrity of the
force field. On another note, when using pressure coupling, taking
half the box size for rvdw may make the simulation fail pretty quickly
if the box contracts (and we'll get another question on this list...).

>
> <The cut-off length is longer than half the shortest box vector or longer
> <than the smallest box diagonal element. Increase the box size or decrease
>>rvdw.
>

The answer of Justin was right on, set a larger distance between
periodic images. If -d doesn't serve you well, because the solute is
to small, set the box dimensions using the option '-box' :)

Cheers,

Tsjerk

> --
> Vitaly V. Chaban
> School of Chemistry
> National University of Kharkiv
> Svoboda sq., 4, Kharkiv 61077, Ukraine
> email: chaban at univer.kharkov.ua
> skype: vvchaban
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623