<div dir="ltr"><div><div><div><div>Hi,<br><br></div>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 Gromacs.<br><br></div>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 part.<br><br></div>Thanks,<br></div>Isaac<br></div><div class="gmail_extra"><br><div class="gmail_quote">2016-09-07 14:35 GMT+02:00 Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi,<br>
<br>
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.<br>
<br>
Cheers,<br>
<br>
Berk<div><div class="h5"><br>
<br>
On 2016-09-07 14:15, Yi Isaac Yang wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>Hi Berk,<br>
<br>
</div>
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.<br>
<br>
</div>
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).<br>
<br>
</div>
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. <br>
<br>
</div>
Thank you and best regrads,<br>
</div>
Isaac<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2016-09-07 12:17 GMT+02:00 Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi,<br>
<br>
Please don't send the same mail multiple times.<br>
<br>
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.<br>
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).<br>
<br>
Cheers,<br>
<br>
Berk
<div>
<div><br>
<br>
On 2016-09-07 11:46, Yi Isaac Yang wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">Dear developers, <br>
<br>
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? <br>
<br>
Thank you very much and best regards, <br>
Isaac <br>
</div>
<br>
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