[gmx-users] Values for pairs, when attached to the topology...?

Berk Hess gmx3 at hotmail.com
Fri May 13 17:53:35 CEST 2005

>From: Maik Goette <mgoette at mpi-bpc.mpg.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Values for pairs, when attached to the 
>Date: Fri, 13 May 2005 17:16:32 +0200
>Hi Berk
>Thanks for the fast answer...
>Does this mean, that gromacs recognizes one pair of parameters after the 2 
>atom numbers in the pairs section as B-Values, not as A?


>For its perhaps easier to script it, am I allowed to enter both A and B 
>values after the 2 atom numbers, even if the parameters don't change? It's 
>much easier to calculate c6 and c12 out of eps and sig, than to let the 
>script attach just the changed parameters, I think.
>Hmmm...I don't exactly understand, what the last part means...Does it mean, 
>that I am able to include B-parameters via pdb2gmx ?
>It only makes sense to me, to change atom types, or create new ones, when 
>pdb2gmx is able to do the above...
>And for I started questioning....;)
>Have the bonded parameters of perturbed atoms to be inserted, when nothing 
>on the bonds or angles changes?

I mean that in OPLS all bonded parameters are defined by atom type.
If you change the atom type in topology B, grompp will get the correct
parameters for topologies A and B when you have enetered no parameters
at all in the molecule section.


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