[gmx-users] RE: grompp and box size

[Vitaly Chaban]

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.


-- 
Vitaly

2008/8/9 Tsjerk Wassenaar <tsjerkw at gmail.com>:
> 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
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
> 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
>