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

Albert Solernou a.solernou at leeds.ac.uk
Tue May 12 13:57:41 CEST 2015

Thanks Justin,
still I would not know how to go from a .edr file into a trajectory that 
has the forces of the atoms I am interested in.


On 05/12/2015 12:48 PM, Justin Lemkul wrote:
> On 5/12/15 7:46 AM, Albert Solernou wrote:
>> 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?
> The nonbonded terms don't depend on the bonded terms; they are, by 
> default, saved in the .edr file.  If you want some group-wise 
> decomposition (e.g. interaction energy) then that's what energygrps 
> are for.  There is no need to modify code or hack the topology at all 
> if this is what you're after.
> -Justin

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

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