[gmx-users] Re.: genion doubt (manjula kasinathan)

Dear manjula kasinathan There aren't the "warning" parameter in gromacs, please remove the warning option in your mdp, if you need, add the flag -maxwarn in the grompp command, grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr -maxwarn 10 your simulation presents Lincs warnings, read the gromacs

[gmx-users] Enc: 1-4 ineractions in double precision

Hi justin; I'm grateful for your help, but unfortunately I didn't solve the problem. I made a change in my mdp file. This is my mdout.mdp: == ; ;File 'mdout.mdp' was generated ;By

[gmx-users] 1-4 ineractions in double precision

Dear Gromacs users; I have got a problem when performing molecular dynamics calculations in double precision with Gromacs Version 4.0.7. My system contains a protein with 482 residues, water molecules and Cl-ions. I have already carried out this same calculation in single precision with succ

[gmx-users] Including K+ in gromos96

"Date: Mon, 6 Jul 2009 16:52:51 -0500 From: sadhna joshi Subject: [gmx-users] including K ion in gromos96 To: gmx-users@gromacs.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" hi, I am using gromacs 3.3.1 and ions.itp does not have K ion (in gromos96). I tried to include it

[gmx-users] Charge pertubation

Hi all, There are a gromacs's program  for  introducing a charge value in residue or make  modifications in the topology file?? How analises the residue's charge of a protein? Thank you Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com__

[gmx-users] Thank you

Dear Justin; Thank you very much, your answers solved my questions, but ocurred new errors which will resolve to further. I go try new parameters create for PVC's atoms now. Thank you Jessé da Nóbrega Graduating in pharmacy from the Federal University of Paraíba - Brazil Veja quais são

[gmx-users] building Topologies

Hi gmx-users, I have trying build topologies for PVC polymer in opls/aa forcefield. I read the chapter 5 and modified the files ffoplsaa.rtp, ffoplsaa.hdb, ffoplsaa-n.tdb, ffoplsaa-c.tdb, but not successful. Below, you can see the blocks that built. The parameters for the residue may seem confu