<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style id="owaParaStyle" type="text/css">P {margin-top:0;margin-bottom:0;}</style>
</head>
<body ocsi="0" fpstyle="1">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Gianluca,<br>
<br>
You might want to take a look at GromPy (https://github.com/GromPy/GromPy).<br>
This is a python interface to the GROMACS library. Amongst other applications, there is an option to perform grand-canonical Monte Carlo using GromPy. The necessary energy evaluations are performed using direct library calls to GROMACS. In this way it is possible
to get around the possibly prohibitive file I/O in shell implementations that use the GROMACS executables. A paper on GromPy and GromPy/GCMC has recently been accepted in JCC, so more details will follow. In the meantime you can have a look at the code and
the tutorial on the above website.<br>
<br>
Good luck!<br>
<br>
Cheers,<br>
Rene
<div><br>
<div style="font-family: Tahoma; font-size: 13px;"><span style="font-family: Courier New;">=====================================================<br>
René Pool<br>
<br>
Division of Molecular and Computational Toxicology<br>
Department of Chemistry and Pharmaceutical Sciences<br>
Vrije Universiteit Amsterdam<br>
De Boelelaan 1083<br>
1081HV AMSTERDAM, the Netherlands<br>
-----<br>
IBIVU/Bioinformatics<br>
Department of Computer Science<br>
Vrije Universiteit Amsterdam<br>
De Boelelaan 1081a<br>
1081HV AMSTERDAM, the Netherlands<br>
<br>
Room P 2.75<br>
E: r.pool@vu.nl<br>
T: +31 20 598 76 12<br>
F: +31 20 598 76 10<br>
=====================================================<br>
</span></div>
</div>
<div style="font-family: Times New Roman; color: rgb(0, 0, 0); font-size: 16px;">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF263923"><font size="2" color="#000000" face="Tahoma"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of Rodrigo Faccioli [rodrigo_faccioli@uol.com.br]<br>
<b>Sent:</b> 24 January 2012 05:29<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent<br>
</font><br>
</div>
<div></div>
<div>Hi Gianluca,<br>
<br>
I forgot to say that the step of compute the energies is considered from pdb2gmx until g_energy.<br>
<br>
Sorry about my oblivion.<br>
<br>
Best regards,<br>
<br>
--<br>
Rodrigo Antonio Faccioli<br>
Ph.D Student in Electrical Engineering<br>
University of Sao Paulo - USP<br>
Engineering School of Sao Carlos - EESC<br>
Department of Electrical Engineering - SEL<br>
Intelligent System in Structure Bioinformatics<br>
<a href="http://laips.sel.eesc.usp.br" target="_blank">http://laips.sel.eesc.usp.br</a><br>
Phone: 55 (16) 3373-9366 Ext 229<br>
Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">
http://lattes.cnpq.br/1025157978990218</a><br>
Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5" target="_blank">
http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5</a><br>
<br>
<br>
<div class="gmail_quote">On Tue, Jan 24, 2012 at 1:07 AM, Rodrigo Faccioli <span dir="ltr">
<<a href="mailto:rodrigo_faccioli@uol.com.br" target="_blank">rodrigo_faccioli@uol.com.br</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Gianluca,<br>
<br>
Thanks your question.<br>
<br>
All steps to obtain a generation with 200 individuals, on average, is 6 minutes for 1VII, example. In each generation I must converted my proteins Dihedral to Cartesian representation, compute the energies, choose the individuals which will go to reproduction,
save previous population. This test was using one core of a conventional Desktop computer.<br>
<br>
The proteins, that I have tested my algorithm<span lang="en"><span></span></span>,
<span lang="en"><span>vary </span><span>from 20 to 56</span> <span>amino</span> <span>
acids</span></span>. <br>
<div class="im HOEnZb"><br>
Best regards,<br>
<br clear="all">
--<br>
Rodrigo Antonio Faccioli<br>
Ph.D Student in Electrical Engineering<br>
University of Sao Paulo - USP<br>
Engineering School of Sao Carlos - EESC<br>
Department of Electrical Engineering - SEL<br>
Intelligent System in Structure Bioinformatics<br>
<a href="http://laips.sel.eesc.usp.br" target="_blank">http://laips.sel.eesc.usp.br</a><br>
Phone: 55 (16) 3373-9366 Ext 229<br>
Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">
http://lattes.cnpq.br/1025157978990218</a><br>
Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5" target="_blank">
http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5</a><br>
<br>
<br>
</div>
<div class="HOEnZb">
<div class="h5">
<div class="gmail_quote">On Tue, Jan 24, 2012 at 12:36 AM, Gianluca Interlandi <span dir="ltr">
<<a href="mailto:gianluca@u.washington.edu" target="_blank">gianluca@u.washington.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks Enrico!<br>
<br>
Just wondering. How fast is it? Calling gromacs must have a lot of overhead. Also, do you call mdrun or does g_energy evaluate the energy?<span><font color="#888888"><br>
<br>
Gianluca</font></span>
<div>
<div><br>
<br>
On Tue, 24 Jan 2012, Rodrigo Faccioli wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
<br>
Although I don't work with MC simulation, I have used Gromacs to obtain energies and others<br>
protein features in my Evolutionary Algorithms (EA).<br>
<br>
In general lines, I created a script that calls Gromacs programs and the output of these<br>
programs, such as g_energy (I read its xvg file), I stored it at a specific file which is<br>
read by my algorithm and its values are put into my data structure. I call Gromacs either<br>
implicit or explicit solvent. <br>
<br>
My project is working with EA until now. However, the integration with GROMACS is able to<br>
work with other kind of algorithms such as MC. Actually, we have idea to work with MC. But,<br>
I don't know when it will be possible. If you want, we can talk about join these work.<br>
<br>
Best regards,<br>
<br>
--<br>
Rodrigo Antonio Faccioli<br>
Ph.D Student in Electrical Engineering<br>
University of Sao Paulo - USP<br>
Engineering School of Sao Carlos - EESC<br>
Department of Electrical Engineering - SEL<br>
Intelligent System in Structure Bioinformatics<br>
<a href="http://laips.sel.eesc.usp.br" target="_blank">http://laips.sel.eesc.usp.br</a><br>
Phone: 55 (16) 3373-9366 Ext 229<br>
Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">
http://lattes.cnpq.br/<u></u>1025157978990218</a><br>
Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5" target="_blank">
http://br.linkedin.com/pub/<u></u>rodrigo-faccioli/7/589/a5</a><br>
<br>
<br>
On Mon, Jan 23, 2012 at 11:39 PM, Gianluca Interlandi <<a href="mailto:gianluca@u.washington.edu" target="_blank">gianluca@u.washington.edu</a>> wrote:<br>
Hi!<br>
<br>
I would like to use gromacs to perform Monte Carlo simulations in implicit<br>
solvent of a protein near a surface. The protein is treated as a rigid body<br>
whereas the surface is fix.<br>
<br>
I see that there are plans to code MC into gromacs:<br>
<br>
<a href="http://www.gromacs.org/Developer_Zone/Programming_Guide/Monte_Carlo" target="_blank">http://www.gromacs.org/<u></u>Developer_Zone/Programming_<u></u>Guide/Monte_Carlo</a><br>
<br>
Is there a preliminary version?<br>
<br>
If not, I wonder whether anybody has tried to do MC with gromacs using IMD and<br>
MDDriver:<br>
<br>
<a href="http://www.baaden.ibpc.fr/projects/mddriver/" target="_blank">http://www.baaden.ibpc.fr/<u></u>projects/mddriver/</a><br>
<br>
Besides this. Is there an easy way to obtain the force field energy of a system<br>
using gromacs? Would I have to run a 0-steps MD and read out the energy? I know<br>
that this would have a big overhead in a MC simulation, but it might be worth<br>
trying.<br>
<br>
Thanks,<br>
<br>
Gianluca<br>
<br>
------------------------------<u></u>-----------------------<br>
Gianluca Interlandi, PhD <a href="mailto:gianluca@u.washington.edu" target="_blank">
gianluca@u.washington.edu</a><br>
<a href="tel:%2B1%20%28206%29%20685%204435" value="+12066854435" target="_blank">+1 (206) 685 4435</a><br>
<a href="http://artemide.bioeng.washington.edu/" target="_blank">http://artemide.bioeng.<u></u>washington.edu/</a><br>
<br>
Postdoc at the Department of Bioengineering<br>
at the University of Washington, Seattle WA U.S.A.<br>
------------------------------<u></u>-----------------------<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or<br>
send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">
http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
<br>
<br>
<br>
<br>
</blockquote>
<br>
------------------------------<u></u>-----------------------<br>
Gianluca Interlandi, PhD <a href="mailto:gianluca@u.washington.edu" target="_blank">
gianluca@u.washington.edu</a><br>
<a href="tel:%2B1%20%28206%29%20685%204435" value="+12066854435" target="_blank">+1 (206) 685 4435</a><br>
<a href="http://artemide.bioeng.washington.edu/" target="_blank">http://artemide.bioeng.<u></u>washington.edu/</a><br>
<br>
Postdoc at the Department of Bioengineering<br>
at the University of Washington, Seattle WA U.S.A.<br>
------------------------------<u></u>-----------------------</div>
</div>
<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">
http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">
gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">
http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</body>
</html>