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
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
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
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 =
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 *
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.
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