[gmx-users] Re Multiple Chain

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 15 22:47:28 CEST 2010

C Johnson wrote:
> For the single chain wiki, what is it talking about then?
> http://www.gromacs.org/Documentation/How-tos/Multiple_Chains
> It seems to me that one would be able to use the single chain pdb file.

"You can just increase that counter from 1 to whatever you require, and then use 
this .top file with a coordinate file with a corresponding number of chains as 
input to grompp."

The key is to have a *corresponding number of chains* in the coordinate file. 
Think of this analogy:  when you add waters with genbox, you (usually) get 
several thousand SOL molecules.  You can't simply have one water molecule in the 
coordinate file and expect it to be represented by something the topology says.

The .top file dictates exactly what is contained in the system; the coordinate 
file dictates where those molecules are in space.  The two files are complementary.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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