Thanks Enrico!
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?
Gianluca
On Tue, 24 Jan 2012, Rodrigo Faccioli wrote:
Hi,
Although I don't work with MC simulation, I have used Gromacs to obtain
energies and others
protein features in my Evolutionary Algorithms (EA).
In general lines, I created a script that calls Gromacs programs and the output
of these
programs, such as g_energy (I read its xvg file), I stored it at a specific
file which is
read by my algorithm and its values are put into my data structure. I call
Gromacs either
implicit or explicit solvent.
My project is working with EA until now. However, the integration with GROMACS
is able to
work with other kind of algorithms such as MC. Actually, we have idea to work
with MC. But,
I don't know when it will be possible. If you want, we can talk about join
these work.
Best regards,
--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
On Mon, Jan 23, 2012 at 11:39 PM, Gianluca Interlandi
<gianl...@u.washington.edu> wrote:
Hi!
I would like to use gromacs to perform Monte Carlo simulations in implicit
solvent of a protein near a surface. The protein is treated as a rigid
body
whereas the surface is fix.
I see that there are plans to code MC into gromacs:
http://www.gromacs.org/Developer_Zone/Programming_Guide/Monte_Carlo
Is there a preliminary version?
If not, I wonder whether anybody has tried to do MC with gromacs using
IMD and
MDDriver:
http://www.baaden.ibpc.fr/projects/mddriver/
Besides this. Is there an easy way to obtain the force field energy of a
system
using gromacs? Would I have to run a 0-steps MD and read out the energy?
I know
that this would have a big overhead in a MC simulation, but it might be
worth
trying.
Thanks,
Gianluca
-----------------------------------------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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-----------------------------------------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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