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By the way, the tutorial can be found on the wiki page at<br>
<a class="moz-txt-link-freetext" href="https://github.com/GromPy/GromPy/wiki/Tutorial:-Using-GromPy-in-GCMC-mode">https://github.com/GromPy/GromPy/wiki/Tutorial:-Using-GromPy-in-GCMC-mode</a>.<br>
<pre class="moz-signature" cols="72">=====================================================
René Pool
Division of Molecular and Computational Toxicology
Department of Chemistry and Pharmaceutical Sciences
Vrije Universiteit Amsterdam
De Boelelaan 1083
1081HV AMSTERDAM, the Netherlands
-----
IBIVU/Bioinformatics
Department of Computer Science
Vrije Universiteit Amsterdam
De Boelelaan 1081a
1081HV AMSTERDAM, the Netherlands
Room P 2.75
E: <a class="moz-txt-link-abbreviated" href="mailto:r.pool@vu.nl">r.pool@vu.nl</a>
T: +31 20 598 76 12
F: +31 20 598 76 10
=====================================================
</pre>
<br>
On 01/24/2012 09:30 AM, Pool, R. wrote:
<blockquote
cite="mid:9C54910E4D1CFE45AFAB946BB576F1836562AE47@PEXMB002A.vu.local"
type="cite">
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charset=ISO-8859-1">
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<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
(<a class="moz-txt-link-freetext" href="https://github.com/GromPy/GromPy">https://github.com/GromPy/GromPy</a>).<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: <a class="moz-txt-link-abbreviated" href="mailto:r.pool@vu.nl">r.pool@vu.nl</a><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
color="#000000" face="Tahoma" size="2"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] on behalf of Rodrigo
Faccioli [<a class="moz-txt-link-abbreviated" href="mailto:rodrigo_faccioli@uol.com.br">rodrigo_faccioli@uol.com.br</a>]<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>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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://lattes.cnpq.br/1025157978990218"
target="_blank">
http://lattes.cnpq.br/1025157978990218</a><br>
Public Profile - <a moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://lattes.cnpq.br/1025157978990218"
target="_blank">
http://lattes.cnpq.br/1025157978990218</a><br>
Public Profile - <a moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
href="http://lattes.cnpq.br/1025157978990218"
target="_blank">
http://lattes.cnpq.br/1025157978990218</a><br>
Public Profile - <a
moz-do-not-send="true"
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>
On Mon, Jan 23, 2012 at 11:39 PM, Gianluca
Interlandi <<a moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://www.gromacs.org/Developer_Zone/Programming_Guide/Monte_Carlo"
target="_blank">http://www.gromacs.org/Developer_Zone/Programming_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 moz-do-not-send="true"
href="http://www.baaden.ibpc.fr/projects/mddriver/"
target="_blank">http://www.baaden.ibpc.fr/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>
-----------------------------------------------------<br>
Gianluca Interlandi, PhD <a
moz-do-not-send="true"
href="mailto:gianluca@u.washington.edu"
target="_blank">
gianluca@u.washington.edu</a><br>
<a
moz-do-not-send="true"
href="tel:%2B1%20%28206%29%20685%204435"
value="+12066854435" target="_blank">+1
(206) 685 4435</a><br>
<a
moz-do-not-send="true"
href="http://artemide.bioeng.washington.edu/"
target="_blank">http://artemide.bioeng.washington.edu/</a><br>
<br>
Postdoc at the Department of
Bioengineering<br>
at the University of Washington,
Seattle WA U.S.A.<br>
-----------------------------------------------------<br>
--<br>
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<br>
<br>
<br>
</blockquote>
<br>
-----------------------------------------------------<br>
Gianluca Interlandi, PhD <a
moz-do-not-send="true"
href="mailto:gianluca@u.washington.edu"
target="_blank">
gianluca@u.washington.edu</a><br>
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<a moz-do-not-send="true"
href="http://artemide.bioeng.washington.edu/" target="_blank">http://artemide.bioeng.washington.edu/</a><br>
<br>
Postdoc at the Department of Bioengineering<br>
at the University of Washington, Seattle WA
U.S.A.<br>
-----------------------------------------------------</div>
</div>
<br>
--<br>
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