[gmx-users] About the parameter in em.mdp..

Dear users, I am running the simulation for 100 ns , 10 ns of each. I have limited space in my a/c. (5 GB). If i will give the frequency of nstxout, nstvout, and nstxtcout 4000 or 5000 steps for every 10 ns simulation, Is that okay for the analysis or it will too long for good simulation analys

[gmx-users] About gromacs run...

Dear users,Happy new yera to all. I have just a very simple query..I am running a simulation for 100 ns. I have decided to run it by 10 ns step of each. In every run, the gromacs generated confout.gro file, the traj.trr, traj.xtc, md.log , ener.edr file, state.cpt etc. The next time when i run t

[gmx-users] calculaton of electrostatic potential

Hi all, I want to calculate the electrostatic potential of my simulated membrane system (DMPC). I think, I need to make an index file for this purpose. Isn't it? In that case, how could I make the selection, I mean i have to select the whole membrane group or I have to create an index file with

[gmx-users] How to calculate PN vector head group angle...

Hello gromacs experts, I want to calculate the PN vector angular distribution along the bilayer axis. I am currently using gromacs 4.0.5 version. Is there any tools in gromacs which one I can use to calculate this properties? If not, anyone pls tell me how can I proceed? I am actually quiet new

Fw: [gmx-users] gromacs..

Hi there, Thanks for telling how to calculate the area per lipid. But at the same time if I want to draw a plot of area per lipid vs time then how can I proceed? Any gromacs tool comes out which I can use? thanks Henry From: Justin A. Lemkul To: Discussio

Re: [gmx-users] gromacs..

Hi there, Thanks for telling how to calculate the area per lipid. But at the same time if I want to draw a plot of area per lipid vs time then how can I proceed? Any gromacs tool comes out which I can use? thanks Henry From: Justin A. Lemkul To: Discussion

Re: [gmx-users] xmgrace plot

2009/12/8 Henry Yang Hello everyone, > >I am also new to xmgrace. I have two .xvg file which I have got from the >simulation data analysis. How can I open both of them in one xmgrace graph >with two distinct color? How can I proceed with the comand? > >I know this is very b

[gmx-users] xmgrace plot

Hello everyone, I am also new to xmgrace. I have two .xvg file which I have got from the simulation data analysis. How can I open both of them in one xmgrace graph with two distinct color? How can I proceed with the comand? I know this is very basic but I have to learn! Pls give me response.