[gmx-users] Self-interaction across periodic boundaries

[Paul Buscemi]

Possibly turn pbc off and use nvt 

PB

> On Jul 8, 2019, at 1:31 PM, Salman Zarrini <salman.zarrini at gmail.com> wrote:
> 
> Thanks Mark.
> The problem is that I would like to keep the overall concentration
> constant, so, using a larger box e.g. with 2 times larger lateral box
> dimensions,
> needs me to increase the number of molecules 8 times, so even more likely
> to lead to percolating structures in a larger simulation box.
> 
> Best regards,
> Salman Zarrini
> 
> On Mon, Jul 8, 2019 at 6:24 AM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> 
>> Hi,
>> 
>> If you're trying to model something like it was at infinite dilution using
>> a periodic box, then the size of the box needs to be at least as large as
>> the size of the structure and its effective interaction radius. It seems
>> like your simulation is suggesting at least one of those is larger than you
>> first thought it was :-)
>> 
>> Mark
>> 
>> On Mon, 8 Jul 2019 at 11:58, Salman Zarrini <salman.zarrini at gmail.com>
>> wrote:
>> 
>>> Dear all,
>>> Using MD simulations I expect to observe aggregation among some molecules
>>> solvated in water to have ultimately a droplet out of the molecules. The
>>> aggregates form to some extent in the course of simulation time, however,
>>> after a while the system become kinetically trapped in artificial
>>> percolating aggregates in which the molecules are self-interacting across
>>> the periodic boundaries.
>>> I wonder if there is any possibility to prevent aggregates
>> self-interaction
>>> across periodic boundaries?
>>> 
>>> Thank you,
>>> Salman
>>> --
>>> Best regards,
>>> 
>>> Salman Zarrini
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.