<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 class="h5"><br>
<br>
On 2016-09-07 11:46, Yi Isaac Yang wrote:<br>
</div></div></div><div><div class="h5">
<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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</blockquote>
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</div></div></div>
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