Re: [gmx-users] setting up osmotic gradient across bilayer.

Thank you Dr. Dallas But my concern is setting water concentration difference in exterior and interior of cell membrane not box size adjustment. Is there any way or some scripts available to do so? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Define intermolecular interactions in L-J simulation

> > > Den 2019-10-23 kl. 18:22, skrev Li, Shi: > > Dear GMX users, > > > > I am wondering if there is a way to define the intermolecular interaction > > to simulation a binary LJ system. For example, I have two atoms A and B, > > they share the same LJ parameter, and I want to change the

Re: [gmx-users] setting up osmotic gradient across bilayer.

Elementary chemistry calculation: # molecules = Na*C*V Na = Avagadros number C = concentration V = volume Use that to set the correct number of waters in a given partial box of correct shape and volume to give the target concentration. If you are after something beyond that, and I've

Re: [gmx-users] Average structure from trajectory

Hi, If I understand you, you would like to create an average structure from a molecular dynamics simulation. That kind of structure would be meaningless; I think you should do a cluster analysis in order to find structure clusters in you simulation. El jue., 24 oct. 2019 a las 13:17, Jacek

[gmx-users] Average structure from trajectory

Dear Gromacs Users, I am trying to obtain an average structure in addition to the rmsf from my trajectories. I tried doing that using 'gmx rmsf', but I was not successful yet. Thanks in advance for all suggestions! Best, Jacek Dr. Jacek