Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

2010-01-11 Thread Tsjerk Wassenaar
rsion 4.0.5 => Simulation Broken     (output >      file) (Chih-Ying Lin) > > > -- > > > Message: 1 > Date: Sun, 10 Jan 2010 10:11:17 +0800 > From: Chih-Ying Lin > Subject: [gmx-users] 6LYZ.pdb + Gr

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

2010-01-11 Thread Chih-Ying Lin
Sun, 10 Jan 2010 10:11:17 +0800 From: Chih-Ying Lin Subject: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken To: gmx-users@gromacs.org Message-ID: <5777f3841001091811l41fbe079ida9822609fc8e...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-

Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

2010-01-10 Thread Tsjerk Wassenaar
Hi Lin, First of all, I would suggest sticking to a single processor until you have a protocol that works. Previously you had an issue with the addition of ions to your .top file. In your protocol, it's not mentioned. Have you made sure that issue is cleared? Cheers, Tsjerk On Sun, Jan 10, 2010

Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

2010-01-09 Thread Justin A. Lemkul
On 1/9/10 10:42 PM, Chih-Ying Lin wrote: Hi I did the EM and the potential energy went to the very negative number. But the simulaiton broke in the PR step. Thank you Lin Saying the system broke is useless. There will certainly be some information in the .log file (LINCS warnings, etc). I

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

2010-01-09 Thread Chih-Ying Lin
Hi I did the EM and the potential energy went to the very negative number. But the simulaiton broke in the PR step. Thank you Lin -- 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 befor

Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (output file)

2010-01-09 Thread Itamar Kass
Hi, It is not clear to me if you did EM or not. If you didn't, it is highly advisable to do short EM before you start your PR step. Best, Itamar On Sun, Jan 10, 2010 at 1:29 PM, Chih-Ying Lin wrote: > > Hi > 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running > the simulati

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (output file)

2010-01-09 Thread Chih-Ying Lin
Hi 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the simulation on Gromacs. System = 6LYZ.pdb + CL- + water molecules Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step Positio

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

2010-01-09 Thread Chih-Ying Lin
Hi 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the simulation on Gromacs. System = 6LYZ.pdb + CL- + water molecules Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step Positio