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

Tue May 12 16:19:16 CEST 2015

Great!
 From your last email, I thought there was no way to get what I 
wanted... I'll read carefully chapter 5!

Cheers,
Albert

On 05/12/2015 02:56 PM, Mark Abraham wrote:
> Hi,
>
> Sorry, actually, that won't help you get non-bonded *forces* since there is
> no way to decompose them. You can decompose energies that way. To get the
> forces you want, you need a .tpr that has only non-bonded interactions, and
> to do that correctly, you will have to explicitly list the [exclusions]
> that would otherwise be generated by the bonds, as Justin suggests. See
> chapter 5.
>
> Mark
>
> On Tue, May 12, 2015 at 3:39 PM Albert Solernou <a.solernou at leeds.ac.uk>
> wrote:
>
>> 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
>>>>>>
>>>>>> --
>>>>>> 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
>>>>
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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