[gmx-users] Connections

[Justin Lemkul]

On 1/7/16 9:14 AM, Chiara Bello wrote:
> Hi gromacs users,
>
> I'm trying to simulate a system in which in addition to other molecules there will be a polymer consisting of PMVE/MA linked to PEG chains, this polimer has about 11000 atoms.
>
> I have the itp topology files of the PEG and PMVE/MA monomers and the pdb file of the whole polimer.
>
> Since I am not an expert in the use of gromacs I would avoid changing the files of the force field. So I thought to include these itp file in the top topology file of the system (using the include file mechanism) and add the polymer to the system using insert-molecules.
>
> Is there a way to communicate to gromacs the connections between the monomers of the polymer?
>

Individual .itp files of monomers will not work, because you need bonds between 
them.

See here for the most straightforward method:

http://www.gromacs.org/Documentation/How-tos/Polymers

If you have reliable parameters in the .itp files, this is a simple matter of 
transferring that information into .rtp format.

-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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