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

[Albert Solernou]

Hi Mark,
thanks for that. This was the route that I was taking so far. However, 
and I may be missing something, I don't see how your approach excludes 
the bonded terms from the -rerun calculation.

Thanks,
Albert

On 05/12/2015 01:16 PM, Mark Abraham wrote:
> Hi,
>
> This is one of the things for which mdrun -rerun on a subset trajectory is
> useful. Make the subset trajectory, make the subset topology (including
> keeping bonds plus their associated exclusions, as appropriate) and you'll
> get the forces. tpbconv can make subsets, but YMMV.
>
> Mark
>
> On Tue, May 12, 2015 at 2:12 PM Albert Solernou <a.solernou at leeds.ac.uk>
> wrote:
>
>> Hi,
>> I may have not expressed well my final goal. I need a trajectory, a .trr
>> file, that has the forces. I am interested in the non-bonded forces of a
>> sub-set of the residues, so I need to re-compute these, and cannot use
>> the values that come from the full trajectory where all the residues are
>> present.
>>
>> Thanks for your time,
>> Albert
>>
>> On 05/12/2015 12:59 PM, Justin Lemkul wrote:
>>>
>>> On 5/12/15 7:57 AM, Albert Solernou wrote:
>>>> 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.
>>>>
>>> You don't.  The .edr file is the energy output of a simulation. If you
>>> have your subtrajectory of interest, you'll get a new .edr file with
>>> the quantities you want, if I understand your description.
>>>
>>> -Justin
>>>
>>>> Best,
>>>> Albert
>>>>
>>>>
>>>> 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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-- 
---------------------------------
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451