[gmx-users] Cross-linked Polymer Simulation

[David]

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
format.
-- 
Groeten, David.
________________________________________________________________________
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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