[gmx-users] specifying interaction energy between residues

[Mark Abraham]

----- Original Message -----
From: Gene Polovy <gpolovy at gmail.com>
Date: Saturday, May 22, 2010 11:00
Subject: Re: [gmx-users] specifying interaction energy between residues
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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.

Bad idea. Forcefields were parameterized with particular kinds of values in mind, and if you stray too far from them you will have a tough time defending your conclusions. Read the primary literature for your forcefield, and look at what other people have used for similar recent simulations.
 
> 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 think you can do what you want with user tables (see manual), but your description is still not all that clear. You'll have to do a bunch of legwork understanding what's going on now so that you can change it sensibly. Only once you can explain to someone else how it works now should you think about changing it :-)

Mark

> 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.
> 
> Gene
> 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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