[gmx-users] Running long MD simulation

Justin Lemkul jalemkul at vt.edu
Sun Feb 4 16:00:18 CET 2018

On 2/4/18 9:57 AM, Ahmed Mashaly wrote:
> And the index file? what is the point of inserting them as input for NPT and MD? They should be for the whole system, not certain groups, right? Kind Regards,Ahmed

Please consult basic tutorials that explain the purpose of these files 
for thermostatting, energygrps, etc.


>        From: Justin Lemkul <jalemkul at vt.edu>
>   To: gmx-users at gromacs.org
>   Sent: Sunday, February 4, 2018 4:20 PM
>   Subject: Re: [gmx-users] Running long MD simulation
> On 2/4/18 9:15 AM, Ahmed Mashaly wrote:
>> Thanks Justin.
>> I found this one:
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118282.html
>> 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?
> Checkpoint files are essential for exact continuations. Without them,
> you lose thermodynamic state information, precise velocities, etc.
> Always use a checkpoint.
>> 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?
> You only need to invoke grompp if changing something about the system -
> output settings, ensemble, use of restraints, etc. Otherwise, just
> extend via convert-tpr and mdrun -cpi.
> -Justin


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

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