[gmx-users] rerun under non-bonded E. terms

Albert Solernou 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:
>> Hi,
>> I am getting fairly large values for the LJ energy term (order 10^8), 
>> while
>> 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 
>> these
>> 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.
> -Justin

   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

More information about the gromacs.org_gmx-users mailing list