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On 24/01/2012 3:29 PM, Rodrigo Faccioli wrote:
<blockquote
cite="mid:CAG=yoiHUfBsaJfZ3O2WPJCWbay+kr98RAWTjog5MZ=0wY5jAXg@mail.gmail.com"
type="cite">Hi Gianluca,<br>
<br>
I forgot to say that the step of compute the energies is
considered from pdb2gmx until g_energy.<br>
</blockquote>
<br>
If your topology is not changing, then you need only construct a new
pseudo-trajectory for the n configurations whose energy you want,
and then run mdrun -rerun using the same .tpr every time. Even if
the topology can change, for doing lots of iterates, some kind of
hash will allow you to reuse previously generated .tpr files very
cheaply.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAG=yoiHUfBsaJfZ3O2WPJCWbay+kr98RAWTjog5MZ=0wY5jAXg@mail.gmail.com"
type="cite"><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">rodrigo_faccioli@uol.com.br</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;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:0 0 0
.8ex;border-left:1px #ccc solid;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:0 0
0 .8ex;border-left:1px #ccc
solid;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
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target="_blank">gianluca@u.washington.edu</a><br>
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href="http://artemide.bioeng.washington.edu/"
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<br>
Postdoc at the Department of Bioengineering<br>
at the University of Washington, Seattle WA
U.S.A.<br>
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</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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Postdoc at the Department of Bioengineering<br>
at the University of Washington, Seattle WA U.S.A.<br>
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