[gmx-users] Cross-linked Polymer Simulation
spoel at xray.bmc.uu.se
Fri Jun 27 19:22:01 CEST 2003
On Fri, 2003-06-27 at 17:51, Lee Cheng Siang wrote:
> 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
yes you can! try harder.
gromacs is not designed for this kind of stuff, but it is possible.
> I would appreciate any hints! ANY! Thank you very much.
didn't I just give them?
start with a dimer and use x2top. Modify the ffgmx.n2t file until you
get a topology without errors. Then put in your whole coordinate file.
To get some more hints about the parameters drop a monomer in the prodrg
server for comparison.
Also read chapter 5 of the manual such that you understand the top file
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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