[gmx-users] Topology for Cross linked polymer chains

[sridhar dwadasi]

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 ?

Thank You
Sridhar