RE: [gmx-users] CHARMM36 lipid bilayers

2010-10-22 Thread Berk Hess
a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I

Re: [gmx-users] CHARMM36 lipid bilayers

2010-10-22 Thread Sven Jakobtorweihen
Charmm does. Since the switching range is so long and this is where a large part of the dispersion attraction acts, this might have a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: Re: [gmx-users

Re: [gmx-users] CHARMM36 lipid bilayers

2010-10-22 Thread Thomas Piggot
From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you

Re: [gmx-users] CHARMM36 lipid bilayers

2010-10-22 Thread Pär Bjelkmar
long and this is where a large part of the dispersion attraction acts, this might have a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also

Re: [gmx-users] CHARMM36 lipid bilayers

2010-10-22 Thread Thomas Piggot
...@soton.ac.uk mailto:t.pig...@soton.ac.uk To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running

Re: [gmx-users] CHARMM36 lipid bilayers

2010-10-22 Thread Sven Jakobtorweihen
a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per

RE: [gmx-users] CHARMM36 lipid bilayers

2010-10-21 Thread Berk Hess
Hi, You have very strange and complex cut-off settings in Gromacs. What Charmm settings are you trying to mimic? Berk Date: Thu, 21 Oct 2010 15:03:51 +0200 From: jakobtorwei...@tuhh.de To: gmx-users@gromacs.org Subject: [gmx-users] CHARMM36 lipid bilayers Dear gmx-users, recently Pär

Re: [gmx-users] CHARMM36 lipid bilayers

2010-10-21 Thread Thomas Piggot
Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed