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

[Albert Solernou]

Thanks to you all,
feel free to mark that question as "solved".

Best,
Albert



On 05/12/2015 02:23 PM, Mark Abraham wrote:
> Hi,
>
> Use the nonbonded terms in the .edr files, not the totals.
>
> Mark
>
> On Tue, May 12, 2015 at 2:32 PM Albert Solernou <a.solernou at leeds.ac.uk>
> wrote:
>
>> 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
>>
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>> Gromacs Users mailing list
>>
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-- 
---------------------------------
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451