[gmx-users] Re: Gromacs Help

[Anton Feenstra]

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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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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