[gmx-users] Generating topology file for a long polymer chain

Mahsa E ebadi.mahsa at gmail.com
Sat Aug 5 15:03:32 CEST 2017

Dear gmx-users,

I am trying to build a polymer box from scratch and generate the required
input files. So far, I did these steps:
1. built a chain of the polymer
2. run ACPYPE to generate the topology file...
However, since the chain is long, it took so long time with ACPYPE and the
calculation is timed out without convergence.

- Is it possible to restart the ACPYPE calculation?

I read in some tutorials that it is also possible to run the ACPYPE
calculations for the monomeric unit instead and repeat its parameters for
the whole chain. How is it possible? The polymer chain may have a
conformation with different angles and dihedrals than in the monomer.
In general, how can I use the topology file of a monomer for the longer
chain of a polymer?
Could you please advise me?

Best regards,

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