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

Berk Hess hess at kth.se
Wed Sep 7 14:35:24 CEST 2016


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.



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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