[gmx-developers] Read the component energy and force from the code during simulation
David van der Spoel
spoel at xray.bmc.uu.se
Wed Sep 7 17:03:50 CEST 2016
On 07/09/16 15:44, Yi Isaac Yang wrote:
> Hi,
>
> I know it is not a easy work to split the force, just like what we did
> it in AMBER. In AMBER, we divided the neighbor list into different parts
> at first, just to do this work is so annoying... As you said, I need to
> know the "intimate knowledge of the inner workings of GROMACS". Of
> cause, I am not. So this is the reason why I ask for the help in the
> developer list of Gromacs.
>
> At least, can you tell me how to read the component energy from the
> code? As it can be output in the .edr file, I think it is not so hard to
> read from the codes. Maybe I can start to read the code of Gromacs from
> that part.
>
Here we describe it, in the supporting:
http://dx.doi.org/10.1021/ct400404q
> Thanks,
> Isaac
>
> 2016-09-07 14:35 GMT+02:00 Berk Hess <hess at kth.se <mailto:hess at kth.se>>:
>
> Hi,
>
> In GROMACS is it practically impossible to obtain forces between
> components of the system. To achieve this you would need to modify
> the non-bonded interaction kernels to mask forces based on energy
> group flags. Then you can either all them multiple times with
> different mask or use multiple force outputs if you need maximum
> efficiency. But this requires coding and intimate knowledge of the
> inner workings of GROMACS.
>
> Cheers,
>
> Berk
>
>
> On 2016-09-07 14:15, Yi Isaac Yang wrote:
>> Hi Berk,
>>
>> I am sorry to send so many same mails. Because this is the first
>> time to use the developer list. I didn't receive my mail after I
>> sent it, so I send it again and again.
>>
>> Thank you for reply! Our method is similar as REST (Replica
>> exchange with solute tempering) which just to enhance the solute
>> part of the system but keep the rest of the system as usual.
>> However, our method can't be realized by modified the force field
>> file like in REST (Terakawa et al. JCC 2010: 1228). We must read
>> the intra-energy of solute (marked as U_slu-slu) and the
>> interaction energy between solute and solvent (marked as
>> U_slu-sol) and to modified them. In order to put the modified
>> potential energy into the system, we need to know the component
>> forces caused by the component energy F_slu-slu=-(\partial
>> U_slu-slu)/(\partial r) and F_slu-sol=-(\partial
>> U_slu-sol)/(\partial r).
>>
>> Of cause, I know we cannot divide the whole potential energy into
>> different parts (solute, solvent or interaction energy). Even in
>> AMBER, we just draw the short range interaction of the different
>> parts. However, even if we can only read a part of component
>> energy, at least we can still enhance the sampling of this part.
>>
>> Thank you and best regrads,
>> Isaac
>>
>> 2016-09-07 12:17 GMT+02:00 Berk Hess <hess at kth.se
>> <mailto:hess at kth.se>>:
>>
>> Hi,
>>
>> Please don't send the same mail multiple times.
>>
>> Your request is not clear enough. Do you want forces on
>> different parts of the system or between different parts of
>> the system? The latter is difficult to obtain.
>> Note that with PME, which is what you should be using in most
>> cases, it is difficult, if not impossible, to decompose forces
>> and energies between group (pairs).
>>
>> Cheers,
>>
>> Berk
>>
>>
>> On 2016-09-07 11:46, Yi Isaac Yang wrote:
>>> Dear developers,
>>>
>>> I am developing an enhanced sampling method, and I have
>>> already realized it in AMBER. Now I want to add the code of
>>> this method into Gromacs. This method need to read the
>>> component energy and force of different part of the system
>>> (like protein, solution, etc.) during the simulation.
>>> However, I am not very familiar withe the codes of Gromacs,
>>> so I don't know how to read it. I know when I perform MD
>>> simulation using Gromacs I can set the groups in
>>> "energygrps", then I can read the energy between those groups
>>> in .edr file. So I think it shouldn't be too difficult to
>>> read the component energy and force in the codes. Can you
>>> tell me how to read the component energy and force from the
>>> codes?
>>>
>>> Thank you very much and best regards,
>>> Isaac
>>>
>>>
>>
>>
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>> --
>> Yesterday Young
>> College of Chemistry and Molecular Engineering
>> Peking University
>>
>>
>
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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