[gmx-users] [Fwd: Gromacs Help]
spoel at xray.bmc.uu.se
Fri Jun 27 17:08:01 CEST 2003
>From: Lee Cheng Siang <lee at univ-montp2.fr>
>To: spoel at xray.bmc.uu.se, lpoulsen at chem.au.dk
>Subject: Gromacs Help
>Date: 27 Jun 2003 16:30:25 +0200
>Hello Dr. Spoel and Dr. Poulsen,
>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.
If the polymerization is regular/simple like in a protein then use pdb2gmx, otherwise
use x2top, the latter seems most likely to work. You will have to modify library files,
more in particular I suggest you use copy the file ffgmx.n2t to your working directory
and iteratively run x2top and update the file until you get a topology. You may need a
lot of memory, since the program is O(N^2) in memory IIRC.
>I then submit it to pdb2gmx, it did not work, nor does x2top.
This sort of information is not very helpful, I'm afraid.
>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
>There are a total of 7031 atoms in my PBC box.
>I thank you very much.
>"Sans la liberté de blâmer, il n'est pas d'éloge flatteur" -
C'est tres facile de blâmer
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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