[gmx-users] Re: Gromacs Help
feenstra at chem.vu.nl
Tue Jul 15 09:26:02 CEST 2003
Lee Cheng Siang wrote:
> Hello Dr. Fennstra,
> My name is Kenichi and I'm a graduate student in France doing MD
> simulations on polymer systems. I got your e-mails from the gmx-user
> group while trying to figure out how to build topology files for my
> polymer to get it submitted under Gromacs for MD simulation.
> My polymer is from a bifunctional epoxy monomer which polymerize under
> UV irradiation to produce highly cross-linked polymer structure. I used
> Amorphous Cell from Accelrys to create the PBC box and then I exported
> it to .pdb format.
> I then submit it to pdb2gmx, it did not work, nor does x2top.
> I did not really understand the thread in gmx-user list discussion. So
> may I have some more clarification on how did you manage to solve the
> problem? Or, could you please re-direct me to available ressources for
> my problem, please?
Just back from vacation, I don't know if you already sent this question
to the gmx-users maillist or not. In case not, I cc'ed this mail to the
list. As I am no expert in polymers, I am probably not the best person
to help you on your way with this, I'm afraid.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
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