<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>Besides the CRA moves, I had earlier implemented simple moves for rigid body motion and internal coordinate displacement. I remember Rene Pool was also doing GCMC. So, finding a way to put this all together would be a great start.</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> <br> <b><span style="font-weight: bold;">Enviadas:</span></b> Terça-feira, 31 de Janeiro de 2012 23:53<br> <b><span style="font-weight: bold;">Assunto:</span></b> Re: [gmx-developers] Monte Carlo Simulations<br> </font> </div> <br>Hi, Andre-<br><br>Having an implementation of the CRA moves would be great, since those are<br>complicated. Again, the MAIN problem is putting together a general MC<br>framework for all the different move types -- putting the code into the<br>current framework probably won't be that useful. I'll be keeping track of<br>the interested names; once 4.6 is out the door, we can start talking about<br>the best way to put everything together in 5.0.<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: "André Assunção S. T. Ribeiro" <<a ymailto="mailto:aastr@yahoo.com.br" href="mailto:aastr@yahoo.com.br">aastr@yahoo.com.br</a>><br>> Reply-To: "André Assunção S. T. Ribeiro" <<a ymailto="mailto:aastr@yahoo.com.br" href="mailto:aastr@yahoo.com.br">aastr@yahoo.com.br</a>><br>> Date: Tue, 31 Jan 2012 17:30:13 -0800<br>> To: "<a ymailto="mailto:michael.shirts@virginia.edu" href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a>" <<a ymailto="mailto:michael.shirts@virginia.edu" href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a>>, Discussion<br>> list for GROMACS development <<a ymailto="mailto:gmx-developers@gromacs.org" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>> Subject: Re:
[gmx-developers] Monte Carlo Simulations<br>> <br>> Hi,<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 development<br>> version, if that interests anyone.<br>> <br>> Cheers,<br>> Andre.<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>> 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 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>>>
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