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 <jalem...@vt.edu>
 To: gmx-us...@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.

-Justin

>
>
>        From: Justin Lemkul <jalem...@vt.edu>
>  To: gmx-us...@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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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