[gmx-users] Polymers

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 5 09:10:52 CEST 2014

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.


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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