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Hi,<br>
<br>
GromPy is compatible with gmx 4.0.7. There are plans to port it to
higher gmx versions, but I do not know when that will happen.<br>
<br>
Cheers,<br>
René<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 01/25/2012 06:53 AM, Kiwoong Kim wrote:
<blockquote
cite="mid:CAKuZkRwcL30k58hz6L40K3Uz-DBP4rTQuiipB=S0Li085yMh_w@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
Grompy looks like fancy. <br>
Is it reliable for conducting GCMC?? <br>
<br>
I also need to perform GCMC along with MD. <br>
<br>
In Grompy, it seems that the Grompy is compatible with gromacs
4.0.5. <br>
The version of gromacs I use is 4.5.X.<br>
Is it possible to use Grompy with my Gromacs??<br>
<br>
<br>
<div class="gmail_quote">2012/1/25 Gianluca Interlandi <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:gianluca@u.washington.edu">gianluca@u.washington.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Renè,<br>
<br>
This might be a silly question. In the documentation of GromPy
it says that:<br>
<br>
"The system consists of mono-atomic water molceules defined in
the MARTINI force field. The intermolecular interactions
between such molecules are modelled using the Lennard-Jones
potential only."<br>
<br>
My system is all-atom and all-hydrogen and I need to use the
GBSA solvation model. Is it still going to work, or is the
tutorial just an example of what you can do with GromPy?<br>
<br>
Thanks,<br>
<br>
Gianluca
<div>
<div class="h5"><br>
<br>
On Tue, 24 Jan 2012, René Pool wrote:<br>
<br>
</div>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div class="h5">
By the way, the tutorial can be found on the wiki page
at<br>
<a moz-do-not-send="true"
href="https://github.com/GromPy/GromPy/wiki/Tutorial:-Using-GromPy-in-GCMC-mode"
target="_blank">https://github.com/GromPy/GromPy/wiki/Tutorial:-Using-GromPy-in-GCMC-mode</a>.<br>
<br>
=====================================================<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 moz-do-not-send="true" href="mailto:r.pool@vu.nl"
target="_blank">r.pool@vu.nl</a><br>
T: +31 20 598 76 12<br>
F: +31 20 598 76 10<br>
=====================================================<br>
<br>
On 01/24/2012 09:30 AM, Pool, R. wrote:<br>
Hi Gianluca,<br>
<br>
You might want to take a look at GromPy<br>
(<a moz-do-not-send="true"
href="https://github.com/GromPy/GromPy"
target="_blank">https://github.com/GromPy/GromPy</a>).<br>
This is a python interface to the GROMACS library.
Amongst other<br>
applications, there is an option to perform
grand-canonical Monte Carlo<br>
using GromPy. The necessary energy evaluations are
performed using direct<br>
library calls to GROMACS. In this way it is
possible to get around the<br>
possibly prohibitive file I/O in shell
implementations that use the<br>
GROMACS executables. A paper on GromPy and
GromPy/GCMC has recently been<br>
accepted in JCC, so more details will follow. In
the meantime you can<br>
have a look at the code and the tutorial on the
above website.<br>
<br>
Good luck!<br>
<br>
Cheers,<br>
Rene<br>
=====================================================<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 moz-do-not-send="true"
href="mailto:r.pool@vu.nl" target="_blank">r.pool@vu.nl</a><br>
T: +31 20 598 76 12<br>
F: +31 20 598 76 10<br>
=====================================================<br>
<br>
</div>
</div>
_____________________________________________________________________________________
<div>
<div class="h5"><br>
From: <a moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a> [<a
moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a>] on
behalf<br>
of Rodrigo Faccioli [<a moz-do-not-send="true"
href="mailto:rodrigo_faccioli@uol.com.br"
target="_blank">rodrigo_faccioli@uol.com.br</a>]<br>
Sent: 24 January 2012 05:29<br>
To: Discussion list for GROMACS users<br>
Subject: Re: [gmx-users] Monte Carlo with Gromacs and
implicit solvent<br>
<br>
Hi Gianluca,<br>
<br>
I forgot to say that the step of compute the energies is
considered from<br>
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>
On Tue, Jan 24, 2012 at 1:07 AM, Rodrigo Faccioli <<a
moz-do-not-send="true"
href="mailto:rodrigo_faccioli@uol.com.br"
target="_blank">rodrigo_faccioli@uol.com.br</a>><br>
wrote:<br>
Hi Gianluca,<br>
<br>
Thanks your question.<br>
<br>
All steps to obtain a generation with 200
individuals, on average,<br>
is 6 minutes for 1VII, example. In each generation
I must <br>
converted my proteins Dihedral to Cartesian
representation, compute<br>
the energies, choose the individuals which will go
to reproduction,<br>
save previous population. This test was using one
core of a<br>
conventional Desktop computer.<br>
<br>
The proteins, that I have tested my algorithm, vary
from 20 to 56<br>
amino acids.<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 -<br>
<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 Tue, Jan 24, 2012 at 12:36 AM, Gianluca Interlandi<br>
<<a moz-do-not-send="true"
href="mailto:gianluca@u.washington.edu"
target="_blank">gianluca@u.washington.edu</a>>
wrote:<br>
Thanks Enrico!<br>
<br>
Just wondering. How fast is it? Calling gromacs
must have a<br>
lot of overhead. Also, do you call mdrun or does
g_energy<br>
evaluate the energy?<br>
<br>
Gianluca<br>
<br>
On Tue, 24 Jan 2012, Rodrigo Faccioli wrote:<br>
<br>
Hi,<br>
<br>
Although I don't work with MC simulation, I
have<br>
used Gromacs to obtain energies and others<br>
protein features in my Evolutionary
Algorithms<br>
(EA).<br>
<br>
In general lines, I created a script that
calls<br>
Gromacs programs and the output of these<br>
programs, such as g_energy (I read its xvg
file),<br>
I stored it at a specific file which is<br>
read by my algorithm and its values are put
into<br>
my data structure. I call Gromacs either<br>
implicit or explicit solvent. <br>
<br>
My project is working with EA until now.
However,<br>
the integration with GROMACS is able to<br>
work with other kind of algorithms such as
MC.<br>
Actually, we have idea to work with MC. But,<br>
I don't know when it will be possible. If you<br>
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 -<br>
<a moz-do-not-send="true"
href="http://lattes.cnpq.br/1025157978990218"
target="_blank">http://lattes.cnpq.br/1025157978990218</a><br>
Public Profile -<br>
<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<br>
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<br>
Carlo simulations in implicit<br>
solvent of a protein near a surface. The<br>
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<br>
gromacs:<br>
<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<br>
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<br>
the force field energy of a system<br>
using gromacs? Would I have to run a
0-steps<br>
MD and read out the energy? I know<br>
that this would have a big overhead in a
MC<br>
simulation, but it might be worth<br>
trying.<br>
<br>
Thanks,<br>
<br>
Gianluca<br>
<br>
<br>
-----------------------------------------------------<br>
Gianluca Interlandi, PhD<br>
<a moz-do-not-send="true"
href="mailto:gianluca@u.washington.edu"
target="_blank">gianluca@u.washington.edu</a><br>
+1 (206) 685 4435<br>
<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<br>
U.S.A.<br>
<br>
-----------------------------------------------------<br>
--<br>
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-----------------------------------------------------<br>
Gianluca Interlandi, PhD <a moz-do-not-send="true"
href="mailto:gianluca@u.washington.edu"
target="_blank">gianluca@u.washington.edu</a><br>
+1 (206) 685 4435<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>
--<br>
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</blockquote>
<div class="HOEnZb">
<div class="h5">
<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>
+1 (206) 685 4435<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>
-----------------------------------------------------</div>
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