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

[Justin Lemkul]

On 8/5/17 8:12 AM, Mahsa E wrote:
> 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?
> 

You parametrize the monomer (charges, atom types, bonded parameters), then build 
up by doing, e.g. conformational energy scans of dihedral rotations between the 
dimer.  That way you can build a proper model of the whole polymer.  Do not try 
to parametrize an entire polymer at once; you'll end up with a 
conformation-specific solution for a given geometry, if you can even get it to 
work at all.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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