[gmx-users] About g_msd. I want to plot the curve from 0.01ps.

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 10 14:52:08 CET 2012

On 10/01/2012 11:21 PM, Kiwoong Kim wrote:
> Hi
> I have been learning how to use gromacs owing to your advice.
> I have simple question on g_msd.
> I tried to plot MSD curve using g_msd. I want to deeply investigate 
> the MSD curve from 0.01ps to the last of simulation (my case, 1ns).
> However, g_msd always produce the MSD curve starting from 1ps.
> How can I adjust the instance of starting time of MSD curve (for 
> example, 0.01ps - 1ns)??

It can't analyze more frames than exist in your trajectory file, which 
you controlled with your .mdp file when you ran the simulation. See what 
gmxcheck has to say about your trajectory file.


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