[gmx-users] Running long MD simulation

Ahmed Mashaly mashaly_1988 at yahoo.com
Sun Feb 4 15:16:35 CET 2018

Thanks Justin.

I found this one:

Another question I have about using cpt

I know checkpoint is important for continuing simulation, but I didn't know that we have to use it also from nvt output to npt input and from npt output to md input ... I was just using the output .gro as input for the next step ... Is this a fatal mistake?

If I have to use it then I can use it with grompp -t prev_checkpoint.cpt or with mdrun -cpi prev_checkpoint.cpt ... Would it be the same result?

Kind Regards,

From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org 
Sent: Friday, February 2, 2018 5:27 PM
Subject: Re: [gmx-users] Running long MD simulation

On 2/1/18 12:45 PM, Ahmed Mashaly wrote:
> Hi
> I want to run a long MD 200 ns, but I want the outputs of every 5 ns to be saved separately ... Is there a way or a script to do this? Kind Regards,Ahmed
It should be very simple with a bash loop and making use of mdrun 
-noappend so you avoid naming clashes. People have done this before and 
posted to the list; just Google within the archive.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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