[gmx-users] pulling along hexane-water interface

Sorry forgot to write the subject in previous mail. Dear gmx-users, We intend to perform free energy calculations by pulling a polypeptide along water-hexane interface. We need to pull the polypypeptide from the water layer towards the hexane layer (crossing the interface). For this we position r

[gmx-users] Re: Problem running free energy simulations

Dear Michael. The simulations at each lambda point starts from the same structure that I equilibrated (NPT ensemble) for 20 nanoseconds. The system has ~7500 atoms in a box the size 5 nm x 5 nm x 5 nm. The molecule of interest is located in the center of the unit cell. Thanks, JErnej > > Sounds

Re: [gmx-users] Re: Problem running free energy simulations

Hmm. This really isn't quite enough information to go on. Can you file a redmine issue, and include the files used to generate the run that crashed (.mdp, .gro,. .top), as well as the files that show it failing (.log)? http://redmine.gromacs.org/ On Thu, Oct 3, 2013 at 4:32 AM, Jernej Zidar wro

[gmx-users] GAFFlipids for Gromacs?

Dear Gromacs users, I have recently written a manuscript titled: "Response of the hydrophilic part of lipid membranes to changing conditions — a critical comparison of simulations to experiments" (http://arxiv.org/abs/1309.2131). To rapidly improve the manuscript further, we started a public blo

[gmx-users] Question regarding g_order

Hi all, I am trying to compute the order parameters for the sn1 and sn2 chains of DOPC (CHARMM36) in bilayer . I am using the g_order tool (v4.6.3). I have constructed for each DOPC chain two index files that contains in the first one all the Carbon atoms where the first Carbon is C=O and the las

Re: [gmx-users] Question regarding g_order

On 10/3/13 11:50 AM, sa wrote: Hi all, I am trying to compute the order parameters for the sn1 and sn2 chains of DOPC (CHARMM36) in bilayer . I am using the g_order tool (v4.6.3). I have constructed for each DOPC chain two index files that contains in the first one all the Carbon atoms where

[gmx-users] double bond

Hi gromacs users, In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6 bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to my C atom. I think, gromacs generate

Re: [gmx-users] double bond

On 10/3/13 3:08 PM, Ehsan Sadeghi wrote: Hi gromacs users, In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6 bonds). When I do energy minimization in vacuum, I got two F atoms nonbon

Re: [gmx-users] double bond

Thanks Justin. I will try different bond parameters. I usually use PyMol or Chimera for visualization. Do you have any recommendation for a visualization software? Cheers, Ehsan - Original Message - From: "Justin Lemkul" To: "Discussion list for GROMACS users" Sent: Thursday, October

Re: [gmx-users] double bond

On 10/3/13 4:15 PM, Ehsan Sadeghi wrote: Thanks Justin. I will try different bond parameters. I usually use PyMol or Chimera for visualization. Do you have any recommendation for a visualization software? For quick visualization, VMD (but it often gets bonds wrong if they are not in line

[gmx-users] Membrane is shifted a lot during umbrella sampling

Dear Gromacs Users/Developers, I am facing problem for doing umbrella sampling simulation for the transferring of a small peptide across a membrene in presence of electric field. Moreover, the simulation was carried out at constant area. Martini force field for protein, lipid and water was used fo