[gmx-developers] Read the component energy and force from the code during simulation
Yi Isaac Yang
yesterday.young at gmail.com
Wed Sep 7 15:45:04 CEST 2016
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
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
2016-09-07 14:35 GMT+02:00 Berk Hess <hess at kth.se>:
> 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,
> 2016-09-07 12:17 GMT+02:00 Berk Hess <hess at kth.se>:
>> 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).
>> 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,
>> Gromacs Developers mailing list
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> Yesterday Young
> College of Chemistry and Molecular Engineering
> Peking University
> Gromacs Developers mailing list
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College of Chemistry and Molecular Engineering
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