Re: [gmx-users] Simulation of ONLY Lipid Bilayer

2010-04-29 Thread Anirban Ghosh
On Thu, Apr 29, 2010 at 3:29 PM, Saumya wrote: > Hi all, > > I am using the pre-equilibriated layers from Tieleman. After the first > energy minimization step, I removed the periodicity using trjconv. Now, in > order to scale the lipid positions, I tried using Inflategro. > Do I need to use stron

[gmx-users] Simulation of ONLY Lipid Bilayer

2010-04-29 Thread Saumya
Hi all, I am using the pre-equilibriated layers from Tieleman. After the first energy minimization step, I removed the periodicity using trjconv. Now, in order to scale the lipid positions, I tried using Inflategro. Do I need to use strong position restraints (because that is for protein and I am

Re: [gmx-users] Simulation of only Lipid Bilayer

2010-04-08 Thread Arun kumar V
On Tue, Apr 6, 2010 at 5:05 PM, Justin A. Lemkul wrote: > > > Arun kumar V wrote: > >> Try PRODRG server to build the molecule as well as to get topology file. >> Though you might have to be careful in using this topology file. >> >> > If by "be careful" you mean "don't use this topology," I'll

Re: [gmx-users] Simulation of only Lipid Bilayer

2010-04-06 Thread Itamar Kass
Hi Saumya, for topology please look at those two paper from Poger in which he derive new parameters for various lipids: 1. Poger D., van Gunsteren W. F. & Mark A. E. (2009) A new force field for simulating phosphatidylcholine bilayers. J. Comput. Chem. in press (doi: 10.1002/jcc.21396) 2.

Re: [gmx-users] Simulation of only Lipid Bilayer

2010-04-06 Thread Justin A. Lemkul
Arun kumar V wrote: Try PRODRG server to build the molecule as well as to get topology file. Though you might have to be careful in using this topology file. If by "be careful" you mean "don't use this topology," I'll agree :) The Gromos parameters for lipids (at least Gromos87 and Gromo

Re: [gmx-users] Simulation of only Lipid Bilayer

2010-04-06 Thread Arun kumar V
Try PRODRG server to build the molecule as well as to get topology file. Though you might have to be careful in using this topology file. Arun Saumya wrote: Hi all, Well, I have been trying to make lipid bilayers using genconf of gromacs from a single lipid molecule. Can anyone tell me how t

[gmx-users] Simulation of only Lipid Bilayer

2010-04-06 Thread Saumya
Hi all, Well, I have been trying to make lipid bilayers using genconf of gromacs from a single lipid molecule. Can anyone tell me how to proceed with the simulation of lipid bilayers starting with a single lipid molecule? How can I obtain the .pdb file for a lipid? Is there any manual that describ