[gmx-users] Cross-linked Polymer Simulation

[Lee Cheng Siang]

Hi,

Objective :
MD Simulation of Epoxy based Cross-linked Polymer Using Gromacs

Polymer :
-Homopolymer
-Highly cross-linked in 3D
-polymerization done using UV radiation

Monomer :
-Two epoxies function at both ends connected by a banal spacer group

Problem :
Mine is a polymer which is higly cross-linked and one of the objective  
in this adventure is to see where these cross-linkings are done in the  
3D matrice of the polymer. Thus, I cannot, say, take one long chain  
(because you cannot define a "chain" for highly cross-linked poplymer)  
and do normal PBC based MD simulation by "dissolving" it with "itself".

Questions :
1) Can I use genconf to filled up a box with my monomers and then try  
to do "polymerization" by hand by joining nearby reactiveepoxy groups?  
If yes, how? Please be concise since I'm a super duper NOVICE.

2) If not, can I use other softwares to generate a cubic box filled  
with my polymers (like using Amorphous Cell under Cerius 2 and  
polymerization done with potential parameters hacking of the force  
field using a home made script), and then export this box to pdb format  
and use it under gromacs? I'm actually doing this, but I'm stuck here.  
I cannot use x2gmx to generate .top file!   How do I generate .top file  
of my box from Cerius 2? Could I use pdb2gmx? How? Which option to use?  
What other files do I need?

The main reason for me to try to use gromacs is due to the "F&F"  
reputation of its code : FAST and FREE. Using Accelrys' Discover  
program, I couldn't  have enough processors running my calculations,  
why? Because we only have 8 licences, and the cost a gigantic BOMB!

I would appreciate any hints! ANY! Thank you very much.

ps: I know that there were threads talking about this problem, but they  
were so fragmented that I didn't understand what was going on at the  
end!

************************************************************************ 
*****

"Sans la liberté de blâmer, il n'est pas d'éloge flatteur" -  
Beaumarchais.

Kenichi ZhenXiang LEE (Alex),
LEMP-MAO,
Université Montpellier 2,
34000 Montpellier, FRANCE.
Tel : 04 67 14 33 66 (laboratoire)
          06 61 43 72 27 (portable)