[gmx-users] Membrane Equilibration

2013-06-11 Thread Neha
Hi everybody, I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman coupling. However, I read that Parinello-Rahman is not great for equilibration so I thought I would do a small run using the Berendsen barostat to decrease the chances of large oscillations. I then used the

Re: [gmx-users] Membrane Equilibration

2013-06-11 Thread Dr. Vitaly Chaban
what happens to your energy before the observed crash? does the crash happen at the same time-step each time? Dr. Vitaly Chaban On Tue, Jun 11, 2013 at 5:22 PM, Neha nshafi...@wesleyan.edu wrote: Hi everybody, I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman

Re: [gmx-users] Membrane Equilibration

2013-06-11 Thread HANNIBAL LECTER
ref_p= 0.0 0.0 ?? Are you sure about this?? On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: what happens to your energy before the observed crash? does the crash happen at the same time-step each time? Dr. Vitaly Chaban On Tue, Jun 11,

Re: [gmx-users] Membrane Equilibration

2013-06-11 Thread Justin Lemkul
On 6/11/13 1:13 PM, HANNIBAL LECTER wrote: ref_p= 0.0 0.0 ?? Are you sure about this?? That's a likely culprit. See below for another. On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: what happens to your energy before the observed