[gmx-users] protein-SWCNT md simulation

Justin Lemkul jalemkul at vt.edu
Mon Feb 4 02:30:47 CET 2013

On 2/3/13 2:17 PM, Atila Petrosian wrote:
> Dear Justin
> Thanks for your reply
>> You're specifying two force fields and hoping they will work together.
>> You need one, unified force field that adequately describes all elements
>> of your system.
> I used only one force field (amber 03) for both of protein and cnt.
>> #include "./cnt.ff/forcefield.itp"
> I used cnt.ff folder for cnt in g_x2top. This folder contains 6 files:
> ffcnt.atp
> ffcnt.rtp
> ffcnt.n2t
> ffcntbon.itp
> ffcntnonbon.itp
> forcefield.itp
> In these files, all parameters for carbon atoms of the cnt were taken
> from type CA for aromatic carbon atoms in the amber 03 force field.
> Thus, I used a single force field.

Then you should be able to properly construct everything you need within Amber03 
rather than having multiple force field #include statements that are potentially 
conflicting or otherwise syntactically ill-formed.

> If my manner is incorrect, please give me more information about correct manner.
> How to do md simulation of the protein-cnt system by gromacs?

The exact details depend upon what you want to do, but the construction of any 
heterogeneous protein-containing system can be done in the same way:

1. Generate protein topology (.top) with pdb2gmx
2. Create topology for other elements using g_x2top or other external software 
and convert them to .itp
3. Include any new topologies from step 2 into system .top (from step 1) using 
#include mechanism
4. Proceed with construction and equilibration



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


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