[gmx-users] dimensions of the box

Justin Lemkul jalemkul at vt.edu
Thu Jan 11 14:08:04 CET 2018

On 1/10/18 12:56 PM, RAHUL SURESH wrote:
> Dear Justin
> I would like to add here something that is happening in my gromacs
> simulation. I am trying to extend timulation to another 50ns. commands as
> follows
> gmx convert-tpr -s alz.tpr -extend 50000 -o extend.tpr
> gmx mdrun -v -deffnm extend -gpu_id 00 -nt 4
> it shows 15 days for the simulation to get over. Normally a 50ns simulation
> takes only around 2 days time in this same system for the same structure.
> Is this common or am I doing something wrong here?
> average ns/day is 8 which was 20 earlier for the same protein.

No idea; check the .log files for the performance summary at the end. 
That will tell you where the most time was taken.



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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