[gmx-users] Topology for Cross linked polymer chains

[Justin Lemkul]

On 3/25/15 2:13 PM, sridhar dwadasi wrote:
> Dear Gromacs Users,
>                                 I have started to use Gromacs recently to
> simulate certain properties of polymer hydrogels. I have taken Poly Vinyl
> Alcohol cross linked with Glutaraldehyde as my system. In this system, I
> have taken two long chains of polymers and cross linked them using
> glutaraldehyde and obtained coordinate file (from Materials Studio) for the
> same.
>                   Currently I am trying to create rtp entries, to create
> topology using pdb2gmx. As the polymer chains are cross linked, I am trying
> to use special bonds file. For this I am defining the cross link structures
> between the two polymer chains as a separate residue and am trying to add
> the bonds between the polymer chains and cross linkers as special bonds (As
> I understood from the manual).
>                    It would be really helpful for me to if anyone can share
> their thoughts/experience on creating topology for crosslinked polymer
> networks. Is the approach mentioned above correct?
>                    Is there any better way to generate topology for such
> systems ?
>

g_x2top is probably better suited for non-linear species.  In principle, 
probably anything could be done with .rtp + specbond.dat, but it depends on the 
total complexity whether or not it is feasible.

-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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