[gmx-users] Polymers

[James]

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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