[gmx-developers] Read the component energy and force from the code during simulation

[Yi Isaac Yang]

Hi David,

I am sorry I make a mistake of your names. Because before that I alway talk
with Berk. I am sorry...

Thank you once again and best regards,
isaac

2016-09-07 14:36 GMT+02:00 David van der Spoel <spoel at xray.bmc.uu.se>:

> On 07/09/16 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.
>>
> I think the problem is ill defined and if you just do the short-range
> parts you are missing all the reaction field due to the solvent at long
> range. By selecting just part of the forces and doing something funny with
> it your dynamics may also be incorrect (that is if you do not strictly have
> F_i = dU/dr_i your dynamics becomes incorrect which you probably need to
> compensate for with a strong T-coupling).
>
> With REST there is a similar problem that only one of the replica's is
> physical, the rest are not. However, even the ensemble at the "physical
> replica" in that case may be skewed by the ensembles at different
> temperatures, especially for short  exchange times I would think.
>
> Does your method work with replica's as well? Can you ascertain that at
> least one replica is completely physical? If not I would advise you to
> reconsider your project. Sorry for the harsh words, but if the physics is
> not consistent the method is not useful.
>
>
>
>> 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
>>
>>
>>
>
> --
> 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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-- 
Yesterday Young
College of Chemistry and Molecular Engineering
Peking University
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