RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-02-01 Thread Pool, R.
am >> 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 >>

RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-31 Thread Gianluca Interlandi
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, f

RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-31 Thread Pool, R.
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 simula

RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-30 Thread Gianluca Interlandi
: 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

RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-30 Thread Pool, R.
_ > 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 solven

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-30 Thread René Pool
>] on behalf of Rodrigo Faccioli [rodrigo_facci...@uol.com.br <mailto: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

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-24 Thread Kiwoong Kim
ciences >> 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 1

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-24 Thread Gianluca Interlandi
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 tha

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-24 Thread Gianluca Interlandi
...@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

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-24 Thread Mark Abraham
On 24/01/2012 12:39 PM, Gianluca Interlandi 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:

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-24 Thread Mark Abraham
On 24/01/2012 3:29 PM, Rodrigo Faccioli wrote: Hi Gianluca, I forgot to say that the step of compute the energies is considered from pdb2gmx until g_energy. If your topology is not changing, then you need only construct a new pseudo-trajectory for the n configurations whose energy you want,

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-24 Thread René Pool
:* 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

RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-24 Thread Pool, R.
= 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

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-23 Thread Rodrigo Faccioli
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 Departmen

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-23 Thread Rodrigo Faccioli
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,

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-23 Thread Gianluca Interlandi
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 energ

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-01-23 Thread Rodrigo Faccioli
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