[gmx-developers] Read the component energy and force from the code during simulation
Yi Isaac Yang
yesterday.young at gmail.com
Wed Sep 7 15:23:19 CEST 2016
About the dynamics, you are right. As we modified the force, the dynamics
become incorrect. Of cause, we have some special way to correct it, but it
is too complicate so we haven't do it yet. In fact, this is one of
disadvantage of our method. However, we usually use our method to calculate
In fact, our method have already published for many years (Yang and Gao.
JCP 2009: 214109). This method is similar to the REST method, but replica
exchange is not needed. This method is much more efficient than REST. We
perform only one trajectory, but this trajectory includes the
thermodynamics of all the replicas of REST. As we only realized this method
in AMBER (Each time when the new edition of AMBER was released, we have to
modified the codes once again), just a few people had used it. Now I want
to transplant this method to Gromacs. I think it will help us to make this
method more popular.
Thank you and best regards,
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,
>> 2016-09-07 12:17 GMT+02:00 Berk Hess <hess at kth.se <mailto: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,
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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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