<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Hi Michael,</span></div><div><span><br></span></div><div><span>I can be mistaken, but, though there are energy-only kernels, I do not remember of an easy way of calculating only a specific set of energy contributions. In MD we always need to calculate everything, but in MC this is not so.</span></div><div><span><br></span></div><div><span>Cheers,</span></div><div><span>Andre.</span></div><div><br></div> <div style="font-size: 12pt; font-family: arial, helvetica, sans-serif; "> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">De:</span></b> "Shirts, Michael (mrs5pt)" <mrs5pt@eservices.virginia.edu><br> <b><span style="font-weight: bold;">Para:</span></b> André Assunção S. T. Ribeiro
<aastr@yahoo.com.br>; Discussion list for GROMACS development <gmx-developers@gromacs.org>; Jared Thompson <thompson.jared.79@gmail.com> <br> <b><span style="font-weight: bold;">Enviadas:</span></b> Quarta-feira, 1 de Fevereiro de 2012 14:19<br> <b><span style="font-weight: bold;">Assunto:</span></b> Re: [gmx-developers] Monte Carlo Simulations<br> </font> </div> <br>Hi, Andre-<br><br>> As Michael said, the main problem would be making a consistent framework for<br>> several MC move types and compatibility with the MD code. Furthermore, for<br>> straight MC simulations, significant changes would need to be made to<br>> energy/force evaluation routines and possibly parallelization routines too.<br><br>There are already inner loops that are energy only, so that's not an issue<br>-- that level of planning has for MC has been around for a while. I don't<br>think the parallelization issues of MC have been thought about as
much, but<br>the current scheme should work fine for a first pass.<br><br>> As to the MC moves, as I said<br>> earlier, the CRA moves and simple moves for rigid body motion and internal<br>> coordinate displacement have been implemented. I am also implementing the<br>> CRRUBAR moves of Betancourt (JCP 2005, JCP 2011). There is oubviously a large<br>> number of other MC moves for various types of molecules that could be<br>> implemented, and if we are able to group of number of people working on this<br>> it would be great.<br><br>Once we get the framework in, I think people can definitely go crazy with<br>the moves. One other aspect of this is being able to validate move sets<br>producing the correct ensemble. I have some code working (hopefully paper<br>sent for review soon) that will be able to do this.<br><br>Best,<br>~~~~~~~~~~~~<br>Michael Shirts<br>Assistant Professor<br>Department of Chemical Engineering<br>University
of Virginia<br><a ymailto="mailto:michael.shirts@virginia.edu" href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a><br>(434)-243-1821<br><br><br>> As to the MC moves, as I said<br>> earlier, the CRA moves and simple moves for rigid body motion and internal<br>> coordinate displacement have been implemented. I am also implementing the<br>> CRRUBAR moves of Betancourt (JCP 2005, JCP 2011). There is oubviously a large<br>> number of other MC moves for various types of molecules that could be<br>> implemented, and if we are able to group of number of people working on this<br>> it would be great.<br>> <br>> Cheers,<br>> Andre.<br>> <br>> <br>> ________________________________<br>> De: Jared Thompson <<a ymailto="mailto:thompson.jared.79@gmail.com" href="mailto:thompson.jared.79@gmail.com">thompson.jared.79@gmail.com</a>><br>> Para: André Assunção S. T. Ribeiro <<a
ymailto="mailto:aastr@yahoo.com.br" href="mailto:aastr@yahoo.com.br">aastr@yahoo.com.br</a>>; Discussion list for<br>> GROMACS development <<a ymailto="mailto:gmx-developers@gromacs.org" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>> Enviadas: Quarta-feira, 1 de Fevereiro de 2012 13:41<br>> Assunto: Re: [gmx-developers] Monte Carlo Simulations<br>> <br>> <br>> Andre,<br>> MC/MD is good, but I was thinking more of a robust, state-of-the-art MC<br>> simulation platform for GROMACS. I would like to have something like this for<br>> my Ph.D. thesis.<br>> <br>> ~j<br>> <br>> <br>> 2012/1/31 André Assunção S. T. Ribeiro <<a ymailto="mailto:aastr@yahoo.com.br" href="mailto:aastr@yahoo.com.br">aastr@yahoo.com.br</a>> <br>> <br>> Hi,<br>>> <br>>> <br>>> Some time ago I sent an email saying that the CRA moves of Ulmschneider
and<br>>> Jorgensen had been implemented in 4.5.3. Since then we have used this code in<br>>> combination with regular MD and the results seem promising. A paper reporting<br>>> our earlier results has been recently published (DOI 10.1002/jcc.22925). The<br>>> code is still based on 4.5.3, but I could put this into the latest<br>>> development version, if that interests anyone.<br>>> <br>>> <br>>> Cheers,<br>>> Andre.<br>>> <br>>> <br>>> <br>>> ________________________________<br>>> De: "Shirts, Michael (mrs5pt)" <<a ymailto="mailto:mrs5pt@eservices.virginia.edu" href="mailto:mrs5pt@eservices.virginia.edu">mrs5pt@eservices.virginia.edu</a>><br>>> Para: Discussion list for GROMACS development <<a ymailto="mailto:gmx-developers@gromacs.org" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>>> Enviadas: Terça-feira, 31
de Janeiro de 2012 22:31<br>>> Assunto: Re: [gmx-developers] Monte Carlo Simulations<br>>> <br>>> <br>>> Hi, all-<br>>> <br>>> MC is definitely an interest of mine, and I think I've already volunteered<br>>> to help organize more MC functionality on the core developer side.<br>>> <br>>> Any MC functionality will be part of 5.0 going forward, and will not be in<br>>> any 4.0 version. The most likely scenario (there's no settled plan yet) is<br>>> to have MC be the parent integrator, and have MD as essentially a<br>>> rejectionless MC variant; this will allow things like hybrid MD/MC, etc.<br>>> The integrator code is too complicated right now, and this will likely be<br>>> part of a larger effort to make the integrators simpler in 5.0.<br>>> <br>>> Right now all<br>> the developers are concentrating very hard on getting 4.6 out<br>>> the
door, so there is not much time to think about it new 5.0 features. But<br>>> definitely ping me about this as soon as you hear about 4.6 being released,<br>>> and we'll start diving in.<br>>> <br>>> The hard part is not WRITING the MC code, it's fitting it into the rest of<br>>> the code in a smooth way.<br>>> <br>>> Best,<br>>> ~~~~~~~~~~~~<br>>> Michael Shirts<br>>> Assistant Professor<br>>> Department of Chemical Engineering<br>>> University of Virginia<br>>> <a ymailto="mailto:michael.shirts@virginia.edu" href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a><br>>> (434)-243-1821<br>>> <br>>> <br>>>> From: Jared Thompson <<a ymailto="mailto:thompson.jared.79@gmail.com" href="mailto:thompson.jared.79@gmail.com">thompson.jared.79@gmail.com</a>><br>>>> Reply-To: Discussion list for GROMACS
development<br>>>> <<a ymailto="mailto:gmx-developers@gromacs.org" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>>>> Date: Tue, 31 Jan 2012 19:00:32 -0500<br>>>> To: <<a ymailto="mailto:gmx-developers@gromacs.org" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>>>> Subject: [gmx-developers] Monte Carlo Simulations<br>>>> <br>>>> Hi All,<br>>>> <br>>>> There has been some discussion in the past with regards to developing a<br>>>> Monte Carlo integrator for the gromacs platform. I recently downloaded and<br>>>> poked through 4.5.5 and I can't find anything in it that looks like a MC<br>>>> integrator function (I'm thinking of do_md). Does anyone have an update on<br>>>> that or what? Does anyone feel like helping me develop a nice MC scheme in<br>>>>
Gromacs?<br>>>> <br>>>> ~j<br>>>> -- <br>>>> gmx-developers mailing list<br>>>> <a ymailto="mailto:gmx-developers@gromacs.org" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>>>> Please don't post (un)subscribe requests to the list. Use the<br>>>> www interface or send it to <a ymailto="mailto:gmx-developers-request@gromacs.org" href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>>> <br>>> --<br>>> gmx-developers mailing list<br>>> <a ymailto="mailto:gmx-developers@gromacs.org" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>>> Please don't post (un)subscribe requests to the list. Use the<br>>> www interface or send it to <a ymailto="mailto:gmx-developers-request@gromacs.org" href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>>> <br>>> <br>>> <br>>> --<br>>> gmx-developers mailing list<br>>> <a ymailto="mailto:gmx-developers@gromacs.org" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>>> Please don't post (un)subscribe requests to the list. Use the<br>>> www interface or send it to <a ymailto="mailto:gmx-developers-request@gromacs.org"
href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>>> <br>> -- <br>> gmx-developers mailing list<br>> <a ymailto="mailto:gmx-developers@gromacs.org" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a ymailto="mailto:gmx-developers-request@gromacs.org" href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br><br><br><br> </div> </div> </div></body></html>