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
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
