Re: [gmx-users] Writing out individual coordinates

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

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

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

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

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

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

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

[gmx-users] Announce: Project - Evolutionary Algorithm with Gromacs, Initial results

: 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] Error when try obtain protein energies instead of system energies

ering 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-facci

[gmx-users] Error when try obtain protein energies instead of system energies

6) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.o

Re: [gmx-users] Doubt about HSD and HSE conformation on Charmm27

tes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Tue, Sep 27, 2011 at 2:10 PM, Justin A. Lemkul wrote: > > > Rodrigo Faccioli wrote: > >> Hi, >> >> I have a doubt about HIS protonation state for chamm

[gmx-users] Doubt about HSD and HSE conformation on Charmm27

g 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-fa

[gmx-users] HIS N Terminal - Charmm27 force field

s.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before postin

Re: [gmx-users] Studying protein folding: An approach

Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Tue, Apr 19, 2011 at 12:53 PM, Miguel Quiliano Meza wrote: > Dear Community. > > I am a beginner user of Gromacs for this reason I would like to consult my > case. > > Nowadays, I am studying a protein which f

Re: [gmx-users] the final structure

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 2011/1/19 ahmet yıldırım

Re: [gmx-users] Error when execute g_energy - the message: not recognized, maybe different CPU?

ile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Fri, Jan 14, 2011 at 12:05 AM, Mark Abraham wrote: > On 14/01/2011 12:12 PM, Rodrigo Faccioli wrote: > >> Hi, >> >> I have an error when try to execute the g_energy program. I'm using >> Gromacs 4.5.

[gmx-users] Error when execute g_energy - the message: not recognized, maybe different CPU?

g 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-facc

Re: [gmx-users] Installation GROMACS UBUNTU

/rodrigo-faccioli/7/589/a5 On Thu, Dec 23, 2010 at 8:12 AM, Sergio Manzetti < sergio.manze...@vestforsk.no> wrote: > > > > > Dear Users, I am unable to get pass the first step of ./configure . This > step works, but when typing "make" it says: > > no

Re: [gmx-users] charmmff

one: 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 Wed, Jul 21, 2010 at 5:34 PM, Sai Pooja wrote: > Hi, > > So you mean it would be easier if one creates a topology file wit

Re: [gmx-users] charmmff

neering - 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 Wed, Jul 21, 2010 at 1:38 PM, Sai Pooja wrote:

Re: [gmx-users] charmmff

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, Jul 20, 2010 at 6:57 PM, Sai Pooja wrote: > Hi, > > If one has to make a version of groma

Re: [gmx-users] Gromacs to APBS

- http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Wed, Jun 30, 2010 at 1:39 PM, Vladimir Lankevich < vladimir.lankev...@gmail.com> wrote: > Dear Gromacs users, > > I need to determine electric potential on each atom,

Re: [gmx-users] Learning MD

://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Mon, May 10, 2010 at 1:57 PM, sonali dhindwal < sonali11dhind...@yahoo.co.in> wrote: > Hello All, > > I am new at MD, and i have started doing it few months ago only. I tried to > run some simulations but taking all the parameters using some

Re: [gmx-users] optimization of gromacs 4.0.5 on AIX Power6

I believe that this problem is about mpi installation. What mpi version was installed ? Lampi or openmpi. There is a good tutorial about that in http://www.gromacs.org/WIKI-import/Quick_and_Dirty_Installation Best regards, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering Unive

Re: [gmx-users] PDB and GRO files

Hi, If I understood your question, do you want to know how can you start a simulation? So, if I'm correct I recommend this link http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this link, there is flowsheet file which is the flowchart to Gromacs simulation. Answered your question

Re: [gmx-users] Where are the good tutorials?

The Gromacs tutorial is a good place for us who is stating. Another place is the Gromacs wiki which has a beginner section ( http://wiki.gromacs.org/index.php/Beginners). In this local, it's possible you to see some videos. I suggest for you read the online manual where has the flow chart and get

[gmx-users] Install on a 64 bit dual core machine - Debian linux

Ricardo, Please, Can you write your error messages? I think that better us understand your situation. Thanks, -- Rodrigo Antonio Faccioli Student of Post-graduation in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineer

[gmx-users] Recompile GROMACS

Hi all, I am studying GROMACS sources and I did some modifications of its source files. So, I would like know how do I recompile GROMACS source. I thanks for any help. Regards, -- Rodrigo Antonio Faccioli Student of Post-graduation in Electrical Engineering University of Sao Paulo - USP Engin

[gmx-users] Install GROMACS - Deb package

Hi, I'm starting my study about GROMACS. So, I have kubuntu linux and I want know: Is there a deb package for me install in my Linux? If there isn't a Deb package, how do I install GROMACS? Thanks! -- Rodrigo Antonio Faccioli Student of Post-graduation in Electrical Engineering University of S