Hi Rene,
Thanks for your reply. One question though. How much overhead do you think
I would have in calling "mdrun -rerun" after every step and would it run
more efficiently if I used GromPy?
Thanks,
Gianluca
On Tue, 31 Jan 2012, Pool, R. wrote:
Hi Gianluca,
Ah, I get it. In that case you can actually use GromPy, but it needs to be modified
slightly. You need only one tpr file that will be stored in memory during execution of
GromPy. For the sampling you can generate new configurations and accept/reject them
according to the appropriate rules. The coordinates/velocities have to be put back in the
"tpr" data structure before calculating the energy. You have to write a routine
that generates a new configuration yourself, but that should not be too hard. Obviously,
the Monte Carlo acceptance rules have to be adjusted for sampling in the NVT ensemble.
The alternative is mdrun -rerun as suggested before.
Cheers,
René
=====================================================
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: r.p...@vu.nl
T: +31 20 598 76 12
F: +31 20 598 76 10
=====================================================
________________________________________
From: Gianluca Interlandi [gianl...@u.washington.edu]
Sent: 30 January 2012 17:36
To: Pool, R.
Cc: Discussion list for GROMACS users
Subject: RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent
Hi René,
I want to perform simulations of a protein near a surface, for example
silicates. The surface is fixed and the protein is treated as a rigid
body. Solvation is treated with GBSA implicit model. The point is to
sample orientations of the protein with respect to the surface using Monte
Carlo moves. I guess I am sampling the canonical ensemble.
Gianluca
On Mon, 30 Jan 2012, Pool, R. wrote:
Hi Gianluca,
The tutorial involves simulations using a simple LJ model. GromPy/GCMC has been
validated by comparing equations of state, calculated using MD in the NVT
ensemble and GromPy in the muVT ensemble, for both the LJ and SPC fluids. For
both models, the muVT and NVT results are in agreement. Therefore, in
principle, you can use GromPy for more sophisticated molecular models.
Which ensemble are you intending to use?
Cheers,
René
=====================================================
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: r.p...@vu.nl
T: +31 20 598 76 12
F: +31 20 598 76 10
=====================================================
________________________________________
From: Gianluca Interlandi [gianl...@u.washington.edu]
Sent: 24 January 2012 21:20
To: Pool, R.; Discussion list for GROMACS users
Subject: Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent
Hi Renè,
This might be a silly question. In the documentation of GromPy it says
that:
"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."
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?
Thanks,
Gianluca
On Tue, 24 Jan 2012, René Pool wrote:
By the way, the tutorial can be found on the wiki page at
https://github.com/GromPy/GromPy/wiki/Tutorial:-Using-GromPy-in-GCMC-mode.
=====================================================
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: r.p...@vu.nl
T: +31 20 598 76 12
F: +31 20 598 76 10
=====================================================
On 01/24/2012 09:30 AM, Pool, R. wrote:
Hi Gianluca,
You might want to take a look at GromPy
(https://github.com/GromPy/GromPy).
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.
Good luck!
Cheers,
Rene
=====================================================
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: r.p...@vu.nl
T: +31 20 598 76 12
F: +31 20 598 76 10
=====================================================
_____________________________________________________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Rodrigo Faccioli [rodrigo_facci...@uol.com.br]
Sent: 24 January 2012 05:29
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent
Hi Gianluca,
I forgot to say that the step of compute the energies is considered from
pdb2gmx until g_energy.
Sorry about my oblivion.
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 Tue, Jan 24, 2012 at 1:07 AM, Rodrigo Faccioli <rodrigo_facci...@uol.com.br>
wrote:
Hi Gianluca,
Thanks your question.
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.
The proteins, that I have tested my algorithm, vary from 20 to 56
amino acids.
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 Tue, Jan 24, 2012 at 12:36 AM, Gianluca Interlandi
<gianl...@u.washington.edu> wrote:
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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-----------------------------------------------------
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.
-----------------------------------------------------
-----------------------------------------------------
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.
-----------------------------------------------------
-----------------------------------------------------
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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