[gmx-users] Run input file prepared by different gmx version

Hi, I prepared a run input file (tpr file) with gromacs 4.07 and can run this tpr on a 4.5.3 installed system. I wonder that there will be a problem about using input files prepared by different gromacs version? Thanks deniz. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

Re: [gmx-users] Converting protonated protein with pdb2gmx

Thanks Justin, I think that I have to write a script to remove hydrogens that are not suitable for united-atom forcefield. After this operation I can use pdb2gmx. On Fri, Oct 29, 2010 at 10:05 PM, Justin A. Lemkul wrote: > > > Deniz KARASU wrote: > >> Hi all, >> &g

[gmx-users] Converting protonated protein with pdb2gmx

Hi all, I'm trying to convert a protein, that is protonated with another special software and by manually checking, with pdb2gmx. I am using FF53A6 forcefield and don't use -ignh option. When I run pdb2gmx it gives me this error. Atom HA in residue VAL 1 not found in rtp entry with 8 atoms

Re: [gmx-users] published paper related to protein simulation using gromacs

Ahmet, For starting you can read Leach's book (Molecular modeling: principles and applications). This book gives you theoretical background and opinion about application areas of molecular dynamics (MD) simulation. Gromacs is only a simulation tool to do MD simulation, after understanding MD you

[gmx-users] deneme

-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.or

Re: [gmx-users] Lipid parameters for GROMOS96 force fields

Hi, I am planing to use 53a6 ff for my membrane protein system. And I can use Kukol 2009 lipid or Roger 2010 lipids so I wonder is there any problem about 53a6 force field and what is the most suitable force field for membrane protein systems? 1) Kukol, A., 2009. Lipid models for united-atom mol

[gmx-users] Best forcefield for DMPC - Protein system

Hi, I am planing to use 53a6 ff for my membrane protein system. And I can use Kukol 2009 lipid or Roger 2010 lipid and topology so I wonder is there any problem about 53a6 force field and what is the most suitable force field for membrane protein systems? I read from http://www.mail-archive.com/

[gmx-users] Best forcefield for DMPC - Protein system

Hi, I am planing to use 53a6 ff for my membrane protein system. And I can use Kukol 2009 lipid or Roger 2010 lipid and topology so I wonder is there any problem about 53a6 force field and what is the most suitable force field for membrane protein systems? I read from http://www.mail-archive.com/

[gmx-users] selenomethionine parameters for ffG53a6

Hi all, Where can I find selenomethionine parameters for ffG53a6 forcefield? Deniz. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe

Re: [gmx-users] Poor load balancing

or such a test. You should run > at least several minutes. The performance you can expect depends > a lot on the interconnect you are using. You will definitely need a > really low-latency interconnect if you have less then 1000 atoms > per core. > > Carsten > > > On Fe

[gmx-users] Poor load balancing

Hi All, I'm trying to d.lzm gromacs benchmarks with 64 node machine, but dynamic load balancing performance is very low. Any suggestion will be of great help. Thanks. Deniz KARASU Log file opened on Sat Feb 13 17:23:37 2010 Host: d077.uybhm.itu.edu.tr pid: 20157 nodeid: 0 nnodes: 6