[gmx-users] on the MDP options

Dear All, In the on-line lysozyme tutorial, it gives a series of mdp files. But it meantioned for different force fields the options should be different. Will you please tell me regardless of force fields, whether all the cutoff-scheme can be Verlet? Besides I can change the rcoulomb and

[gmx-users] Md simulation mdp options error

Hi, I am trying to run a simulation with the following optins in my production mdp file. Previously I have run the simulations with the production run parameters using V-rescale thermostat and berendsen barostat. But now recently I read in discussion that Justin had advised using Parinello-Rahman

Re: [gmx-users] Md simulation mdp options error

On 4/18/14, 4:57 AM, Ankita Naithani wrote: Hi, I am trying to run a simulation with the following optins in my production mdp file. Previously I have run the simulations with the production run parameters using V-rescale thermostat and berendsen barostat. But now recently I read in

Re: [gmx-users] Md simulation mdp options error

Thank you Justin for your reply. Yes indeed this is a production run. So would the following mdp file be okay now? title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= 5000; 0.002 * 5000 = 10 ps or 100 ns dt =

Re: [gmx-users] Md simulation mdp options error

On 4/18/14, 8:55 AM, Ankita Naithani wrote: Thank you Justin for your reply. Yes indeed this is a production run. So would the following mdp file be okay now? title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= 5000; 0.002 *

Re: [gmx-users] Md simulation mdp options error

Also, just one more floating query... In presssure coupling, Previously, I have been using tau_p = 1.0 but for this simulaion, I have changed it to tau_p = 2.0 This was after seeing the mdp file of one of your tutorials. Just wanted to confirm if that's okay. -- Gromacs Users mailing list *