[gmx-users] RE: grompp and box size
chaban at univer.kharkov.ua
Sat Aug 9 21:57:59 CEST 2008
Well, see the paper in which your force field was proposed and type
the exact value of cut-off used by the authors.
I agree with Tsjerk, the answer was not ideal for all the cases but in
the small systems the value of cut-off is practically close to LBOX/2.
It's also close to 1 nm.
2008/8/9 Tsjerk Wassenaar <tsjerkw at gmail.com>:
> 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
> 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' :)
>> 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
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