[gmx-users] Flat-bottomed potential from user-defined reference

[Mark Abraham]

Hi,

Yes, see Justin's answer.

Mark

On Tue, 3 Nov 2015 12:29 Cosseddu, S.M. <s.m.cosseddu at vu.nl> wrote:

> Thanks Vitaly,
>
> However, the manual actually say something slightly different, that is
> "These [restraints] are used to restrain particles to fixed reference
> positions Ri". From a quick look to the sources this is something that
> depends on pos0A and (in certain cases) on  a lambda and pos0B. Please,
> correct me if I am wrong.
>
> From a theoretical point of view the function that computes such
> restraints should be happy with  any reference. With user-defined
> reference, equilibration of the system might be more difficult, and worst
> case scenario everything blows up because of the excessively-strong forces,
> but these are a user issues.
>
> My question is: is there any ways to set pos0A to some user-defined value?
> If this is not possible, it is because of the parallellisation scheme, and
> what is the most suitable method to implement such a spherical
> flat-bottomed potential?
>
> I tried providing grompp with a structure file containing my user-defined
> pos0A via -c (i.e. coords of the relevant atoms were set to the center of
> my sphere), while my initial configuration and velocities were provided via
> -t and a cpt. Unfortunately it  didn't work.
>
> Many thanks
> Salvatore
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Vitaly V.
> Chaban [vvchaban at gmail.com]
> Sent: 03 November 2015 11:47
> To: gmx-users
> Subject: [Spam] Re: [gmx-users] Flat-bottomed potential from user-defined
> reference
>
> Gromacs uses restraints to keep molecules near their original positions.
> See the manual.
>
>
>
>
> On Tue, Nov 3, 2015 at 8:24 AM, Cosseddu, S.M. <s.m.cosseddu at vu.nl> wrote:
>
> > Dear all,
> >
> > I am trying to apply a spherical flat-bottomed potential to maintain some
> > molecules within a certain region. By default, GROMACS uses the initial
> > coordinates as reference. Is there any way to provide different
> references?
> >
> > Many thanks
> > Salvatore
> > --
> > 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.
>