RE: [gmx-users] Membrane simulation with OPLS ff.

2013-09-27 Thread Karthigeyan.Nagarajan
Thanks Justin. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: Thursday, September 26, 2013 7:51 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Membrane simulation with OPLS ff. On 9/26

Re: [gmx-users] Membrane simulation with OPLS ff.

2013-09-27 Thread Oliver Beckstein
On 26 Sep, 2013, at 19:50, Justin Lemkul wrote: > On 9/26/13 10:47 PM, Christopher Neale wrote: >> Dear Karthi: >> >> As far as I am aware, there is no OPLSAA lipid force field. I have used >> Berger lipids with OPLSAA protein >> ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but t

Re: [gmx-users] Membrane simulation with OPLS ff.

2013-09-26 Thread Justin Lemkul
On 9/26/13 10:47 PM, Christopher Neale wrote: Dear Karthi: As far as I am aware, there is no OPLSAA lipid force field. I have used Berger lipids with OPLSAA protein ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing a UA lipid with an AA protein so be aware of pos

Re: [gmx-users] Membrane Simulation

2013-04-18 Thread Justin Lemkul
On 4/18/13 10:59 AM, Giuseppe wrote: Dear all I'm trying to start a simulation with a protein embedded in a bilayer of POPC molecules, but I have some problems when I pack the lipids around the protein. Infact I place the protein in the proper position using the editconf tool with the “-rota

Re: [gmx-users] Membrane simulation - error during EM after inflation step

2013-02-05 Thread Justin Lemkul
On 2/4/13 11:09 PM, John K wrote: Hello Justin, Thank you for providing a tutorial for membrane simulation. I am doing membrane simulation by following your tutorial. When I tried to do energy minimization after inflating the system i got the following result. Steepest Descents converged to m

Re: [gmx-users] membrane simulation

2012-05-03 Thread Justin A. Lemkul
On 5/3/12 10:39 AM, scapr...@uniroma3.it wrote: Than you very much for your reply. I'm using ffnonbonded.itp etc. I still have some doubts regarding to the topology file which has to be used. Should I work and modify the topology file associated with the protein by adding the information relate

Re: [gmx-users] membrane simulation

2012-05-03 Thread Anirban Ghosh
On Thu, May 3, 2012 at 4:38 PM, wrote: > Hi all, > I'm new in Membrane simulations with Gromacs. I have to simulate a system > made up of a protein just leant on a membrane patch which has previously > been extended and made it free of periodicity (with trjconv). I'm reading > the "KALP15 in DPPC