[gmx-users] Running long MD simulation

Ahmed Mashaly mashaly_1988 at yahoo.com
Thu Feb 8 10:08:25 CET 2018

Sorry, I see the point of ndx now ... I thought there was no default group for water_and_ions.
However, the second question is still running through my head Kind Regards,Ahmed 

      From: Ahmed Mashaly <mashaly_1988 at yahoo.com>
 To: "gmx-users at gromacs.org" <gmx-users at gromacs.org> 
 Sent: Thursday, February 8, 2018 9:49 AM
 Subject: Re: [gmx-users] Running long MD simulation
And why don't we modify the .mdp file to be protein_and_JZ4 as the same way you did for water_and_ions instead of making a new index for the list protein_JZ4?
And why do we have some groups duplicated in the default index? for example in the tut, JZ4 was No. 13 and 19, Ion and CL the same, water and SOL the same! Kind Regards,Ahmed Mashaly

      From: Justin Lemkul <jalemkul at vt.edu>
 To: gmx-users at gromacs.org 
 Sent: Sunday, February 4, 2018 4:02 PM
 Subject: Re: [gmx-users] Running long MD simulation

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

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

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


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