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

Yi Isaac Yang yesterday.young at gmail.com
Wed Sep 7 14:16:00 CEST 2016

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>:

> 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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