[gmx-users] rerun under non-bonded E. terms
a.solernou at leeds.ac.uk
Tue May 12 13:46:24 CEST 2015
Well, back to the beginning, then.
Is there a way to do a re-run using only non-bonded energy terms? I'll
explain a bit further. I have a trajectory, and want to get a
(sub)trajectory that has only a sub-set of atoms and that accounts only
for the non-bonded interactions within this sub-set of atoms. So far, I
have the extracted temporary sub-trajectory that contains the solvent
atoms as well as the residues I am interested in. Is there an easy way
to do that? Or should I modify the source code, instead?
On 05/12/2015 12:28 PM, Justin Lemkul wrote:
> On 5/12/15 6:58 AM, Albert Solernou wrote:
>> I am getting fairly large values for the LJ energy term (order 10^8),
>> previous values were much better (order 10^5). I am wondering whether
>> there is a
>> radius decrease for bonded atoms or something equivalent to explain
>> differences. I browsed quickly the manual but could not find any
>> clear explanation.
>> Any ideas?
> It comes from the fact that you're trying to treat everything as
> nonbonded when the functional forms were parametrized with exclusions
> of up to 3 bonds away. If two atoms are bonded, we don't parametrize
> their LJ interactions; they're excluded, so the functional form relies
> on parameters for "normal" nonbonded interactions. Atoms that are
> bonded are usually well within the steep r^12-dominated part of the LJ
> curve. I don't know what your goals are in doing this calculation,
> but they're likely not physically meaningful.
Dr Albert Solernou
EPSRC Research Fellow,
Department of Physics and Astronomy,
University of Leeds
Tel: +44 (0)1133 431451
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