[gmx-users] Polymers

[Tsjerk Wassenaar]

Hi James,

If you care to know more about the algorithm, it is explained in our recent
paper on backmapping in JCTC :)

Cheers,

Tsjerk
On Jun 5, 2014 9:18 AM, "James" <jamesresearching at gmail.com> wrote:

> Hello Tsjerk,
> Thanks, that's very helpful to know.
> Best regards,
> James
>
>
> On 5 June 2014 16:10, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> > Hi James,
> >
> > The top file is only used to generate the run input file. So it has no
> real
> > influence on the run in that sense. For the simulation, every molecule
> > needs to be specified once with all particles and all interactions.
> There's
> > no way around that.
> >
> > Cheers,
> >
> > Tsjerk
> > On Jun 5, 2014 9:00 AM, "James" <jamesresearching at gmail.com> wrote:
> >
> > > Dear Gromacs users,
> > >
> > > I am looking to simulate a polymer with a repeating unit cell. Each
> unit
> > > cell is connected to another unit cell in the same way, with associated
> > > bond and angle restraints, as well as a dihedral force.
> > >
> > > Since [bonds], [angles] and [pairs] etc are specified by atom number,
> it
> > > seems to me that the topology file will become incredibly long if the
> > > polymer is long. I read that one can generate such a system using a
> > > modified .rtp file [1]. If I have understood correctly however, this
> will
> > > still ultimately result in a very long .top file.
> > >
> > > So I would like to ask:
> > > 1. Is a long topology file unavoidable? Is specifying by atom name,
> > rather
> > > than number, not possible?
> > > 2. Will a long .top file impact performance of mdrun?
> > > 3. Is there any limit on the length of the .top file? If not, if anyone
> > has
> > > hit a practical limit (memory, etc), I would be interested to hear
> about
> > > the experience.
> > >
> > > Thank you for your help.
> > > Best regards,
> > > James
> > >
> > > [1] http://www.gromacs.org/Documentation/How-tos/Polymers
> > > --
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