[gmx-users] Re Multiple Chains

C Johnson helstreak at hotmail.com
Thu Sep 16 00:31:51 CEST 2010

This depends entirely upon what your goal is.  Your original question implied 
you wished to build a system of multiple, identical peptides, pertaining to:


Now you want a multimeric protein for which there are multiple, potentially 
different peptide, i.e.:


The approaches are completely different, as the documentation should make quite 
clear.  Simply "having multiple chains" is a very vague statement.  Perhaps if 
you clearly stated your goal for the simulation I (or someone else) could help 
you better.

As for the PDB site, there are probably thousands of proteins in line with what 
you want.  Any heteromultimeric protein would do (assuming, of course, the 
latter case of non-identical chains).


Sorry I wasn't clear.  Basically I want to have a simulation box with as many of the same polypeptide as I can cram in, essentially a simulation of the polypeptide melted.
I would like to see how the polypeptides interact with each other with the ultimate goal of simulating block copolymers.  Since I'm new with Gromacs, I'm just trying
to figure out how to run simulations with multiple chains where all chains are the same type.

Justin, you've been very helpful so far and I appreciate it. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100915/4035d7d5/attachment.html>

More information about the gromacs.org_gmx-users mailing list