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

Nice Job Rodrigo! Your results are very interesting and your implementation of EA algorithm to work with Gromacs is a very relevant contribution. Congratulations! -- Prof. Dr. Alexandre Suman de Araujo Departamento de Física Instituto de Biociências, Letras e Ciências Exatas - IBILCE

Re: [gmx-users] Re: Convert drug Charmm topology to Gromacs

Hi Fabian As far as I know, the way to send your contribution is contacting someone who administrate the website. I think Justin is one of them. Probably some of them are reading us and can help you. Cheers -- Prof. Dr. Alexandre Suman de Araujo Departamento de Física Instituto de

Re: [gmx-users] Convert drug Charmm topology to Gromacs

Why don't you post this in User Contribution area of Gromacs Website? I think this is something that could interest a lot of people. Cheers -- Prof. Dr. Alexandre Suman de Araujo Departamento de Física Instituto de Biociências, Letras e Ciências Exatas - IBILCE Universidade Estadual Pauli

Re: [gmx-users] position restraints and out of bounds atom index

es in .top file is the same I mentioned in the original e-mail. With this, everything worked fine. Cheers ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Un

[gmx-users] position restraints and out of bounds atom index

.itp files. However, I don't know how to do any of these 2 tasks using pdb2gmx. Could anyone help me with this issue? There is any other program in Gromacs package that I should use to fix this problem? Best regards. -- Alexandre Suman de Araujo Instituto de Física de São Carlos Univer

Re: [gmx-users] vanadium non-bonded parameters

4 Cheers ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica

Re: [gmx-users] Problem with removing COM translation

Em 13-08-2010 14:24, ms escreveu: On 12/08/10 15:25, Alexandre Suman de Araujo wrote: I'm simulating a system composed by a protein centered in a sphere of water in vacuum. The water molecules are kept within a virtual sphere with position restrains between oxygen atom and a dummy atom

[gmx-users] Problem with removing COM translation

absolute static COM? Cheers -- ********** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo

Re: [gmx-users] New ion parameters and OPLS-AA

If you decide to change the ions parameters, you can use the method described here: http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255D&searchHistoryKey= It is relatively fast and provide nice parameters. Cheers -- Alexandre Suman de Araujo Insti

Re: [gmx-users] Distance restraint problem with 4.0.5 version

Mark Abraham escreveu: Alexandre Suman de Araujo wrote: Hi Gmxers Some months ago I performed some simulations, with GMX 3.3.3 version, where I apply distance restraint between water oxygen atoms and a static dummy site located at the center of a sphere to keep waters inside this sphere

[gmx-users] Distance restraint problem with 4.0.5 version

n 4.0.5 version compared with 3.3.3 version? Or this can be a bug? Thanks -- ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universida

Re: [gmx-users] PDB and GRO files

y has already done some plugin or script to generate this kind of molecules, try to search in google by "fullerenes and VMD" Cheers -- ** Alexandre Suman de Araujo* Faculdade de Ciências F

Re: [gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU

important programs with unknown people! Cheers -- ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo

Re: [gmx-users] Hg2+ ions in ion.itp

, Eduardo E.) Source: JOURNAL OF PHYSICAL CHEMISTRY BVolume: 111Issue: 9 Pages: 2219-2224 Regards ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto

Re: [gmx-users] use of LAN for parallel processing

Hi Mark Do you know any site/paper/book which clearly discuss the use of other network paradigms (infiniband, myrinet, etc) to perform fair parallel MD simulations? Thanks! ** Alexandre Suman de Araujo

Re: [gmx-users] Drug-Enzyme tutorial- LIE energies in gromacs

nt of new Cd2+ and Pb2+ Lennard-Jones parameters for liquid simulations. J. Phys. Chem. B 2007, 111, (9), 2219-2224. Other references can be found therein. Best regards ** Alexandre Suman de A

Re: [gmx-users] Poor parallel performance in Ubuntu 8.04

Quoting Jussi Lehtola : On Wed, 2009-02-04 at 18:01 -0200, Alexandre Suman de Araujo wrote: Quoting Jussi Lehtola : > That's highly unlikely: it would be a severe performance bug, which > would have been picked up by the kernel packager. > > How did you configure the parallel

[gmx-users] Poor parallel performance in Ubuntu 8.04

anyone already had this problem and solved it. Thanks -- Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil WEBMAIL - IFSC - Instituto de Física de São Carlos

Re: [gmx-users] Software Raid and low GROMACS performance

Hi Martin Martin Höfling escreveu: Am Dienstag, den 20.01.2009, 17:07 -0200 schrieb Alexandre Suman de Araujo: I have two machines with Intel Quad Core processors and Intel motherboards. In the first one I'm running Open Suse with normal partition scheme. In the second I'm runn

[gmx-users] Software Raid and low GROMACS performance

Thank's -- ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química *

Re: [gmx-users] How to treat an isolated iron (Fe 2+)

ling_lists/users.php -- ********** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química

Re: [gmx-users] Possible bug with -rerun option

Thanks David. The instantaneous energies are ok. I'll try to submit this to bugzilla. Best regards Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil David van der Spoel wrote: > Alexandre Suman de Araujo wrote: >> Hi GMXers >> >

[gmx-users] Possible bug with -rerun option

r am I doing something wrong Best regards. -- Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't p

Re: [gmx-users] A simple question about reaction-field

Then the ion-solvent LR interaction is included in ion-solvent SR term in g_energy, am I correct? But what means the LR term that appears when I use rlist< rcoulomb? Thanks David. Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil David van der Sp

[gmx-users] A simple question about reaction-field

the contribution of implicit solvent between rlist and rcoulomb or the contribution of implicit solvent beyond rcloumb, as is said in GMX manual and other reference texts? Thanks -- Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Bra

[gmx-users] Problems in bonded parameters for nitrate with OPLS in GROMACS

O as defined in ffoplsaanb.itp). Are these bond_types correct? If yes, where are the bond parameters for them? Does anybody know the paper where these parameter were published? Thank's -- Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP -

[gmx-users] Nitrate ion

ffoplsaanb.itp). Are these bond_types correct? If yes, where are the bond parameters for them? Does anybody know the paper where these parameter were published? Thank's -- Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP -

Re: [gmx-users] theory of MD

Look at these books: Allen, Tildesley. Computer simulation of liquids Frenkel, Smit. Understanding molecular simulation Leach A.R. Molecular modelling. Principles and applications Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil [EMAIL PROTECTED] wrote

Re: [gmx-users] Locally enhanced sampling

Look at: http://www.gromacs.org/pipermail/gmx-users/2006-January/019356.html Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil Srivastava, Dhiraj (UMC-Student) wrote: > does anyone know how we can do locally enhanced sampling with GROMACS? > &g

Re: [gmx-users] MSD

and 10 ps values for it and see what happen. Well... summarizing... try to run more 5 ns of simulation, run msd using -beginfit from the begin of linear part of your graph, play with t_restart values. I hope I helped you. Cheers Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC -

Re: [gmx-users] MSD and self diffusion

than in the end of it. Like Tsjerk said, attach an image of your output so we can try to help you. Cheers Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil Roman Holomb wrote: Dear all, I have strange MSD graphs when I use g_msd for trajectory anal