[gmx-users] dimensions of the box

[Justin Lemkul]

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

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

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