[gmx-users] specifying interaction energy between residues

Gene Polovy gpolovy at gmail.com
Sat May 22 02:59:34 CEST 2010

I'm trying to simulate three alpha spectrin repeats (R15, R16, R17) using a structure based C-alpha model: http://smog.ucsd.edu/. My task is first to modify the sample .mdp file available at http://smog.ucsd.edu/GromacsTutorial.html. I'm having some difficulty figuring out what to set rlist, rcoulomb and rvdw to. I don't think I need to change anything else except for trying different temperatures? My simulation is running now, but I don't think it's running correctly. I set these parameters somewhat arbitrarily, mainly based on the errors I was getting.

After I get that working, I'd like to somehow provide gromacs with a table that tells it the native interaction energies between different pairs of residues (e.g. ALA & GLN) so that it doesn't assign a generic interaction energy value to all native interactions. (I think it's doing that now.)

I'm a complete newb to gromacs, sorry! I read through most of the manual, but I'm still confused about many of these parameters. I'd really appreciate it if you could help me.

On 2010-05-21, at 5:33 PM, Mark Abraham wrote:

> ----- Original Message -----
> From: Gene Polovy <gpolovy at gmail.com>
> Date: Saturday, May 22, 2010 8:37
> Subject: [gmx-users] specifying interaction energy between residues
> To: gmx-users at gromacs.org
>> Hi There,
>> I'm trying to run a course grained (c alpha) simulation of a 
> Letting us know more about what kind of coarse-grained model you're trying to modify would be useful.
>> protein and I'd like to know how/where I can define 
>> heterogeneous native interaction energies between residues. Is 
>> it under [ pairs ] in the topology file? In other words, I'd 
>> like to use a flavored model rather than a vanilla model. Please help!
> Ah, but we're not sure what your vanilla model is, so it's hard to advise...
> Mark
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