[gmx-users] Problem with Lennard Jones cross terms

Mark Abraham mark.abraham at anu.edu.au
Thu Jul 1 17:16:07 CEST 2010

----- Original Message -----
From: xrysostomos sfhsdfghsdfhsdgh <cbatiss at yahoo.gr>
Date: Friday, July 2, 2010 0:31
Subject: Re: [gmx-users] Problem with Lennard Jones cross terms
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

| > Dear Gaurav
> Thanks a lot for your quick reply
> I have done also what you suggested but the result is the same. I mean that I observe stronger adsorption of the polymers to the surface, when I increased the values of c6 and c12 for Si  in the [atomtypes], but continue having original values in the [ nonbond_params ]. 
> But in general, am I not able with gromacs to switch-off the LJ interactions between the polymers and the substrate?

You are able to. Either you've not done it right, or are observing phenomena unrelated to the LJ interactions. Rather than observe the position of the polymers, which may or may not indicate anything, define suitable energy groups and see what the magnitude of the LJ interactions between those groups actually are.


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