[gmx-users] dimensions of the box

[RAHUL SURESH]

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.

Thank you

On Tue, Jan 9, 2018 at 10:05 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> Thank you all
>
> On Tue, 9 Jan 2018 at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/8/18 6:18 AM, RAHUL SURESH wrote:
>> > Dear all
>> >
>> > For a protein-ligand simulation,
>> >
>> > for the command
>> >
>> > gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 1.0 -c
>> >
>> > Read 680 atoms
>> > Volume: 25.6402 nm^3, corresponds to roughly 11500 electrons
>> > No velocities found
>> >      system size :  3.411 17.359  3.004 (nm)
>> >      diameter    : 17.543               (nm)
>> >      center      :  5.138 15.619  2.935 (nm)
>> >      box vectors :  3.411  2.687  2.798 (nm)
>> >      box angles  :  90.00  90.00  90.00 (degrees)
>> >      box volume  :  25.64               (nm^3)
>> >      shift       :  4.633 -5.847  6.837 (nm)
>> > new center      :  9.771  9.771  9.771 (nm)
>> > new box vectors : 19.543 19.543 19.543 (nm)
>> > new box angles  :  90.00  90.00  90.00 (degrees)
>> > new box volume  :7463.88               (nm^3)
>> >
>> > System size looks so large, which eventually consume more computational
>> > time. For 100ps nvt/npt it takes around 6 hours, which normally gets
>> done
>> > in 3-5 mins..
>>
>> Sounds like you're comparing apples and oranges and hoping for the same
>> result; just because system X runs at a given speed doesn't mean system
>> Y will. You have a system here that is extended along the y-axis,
>> requiring a huge box. That's inherently going to run pretty slow, since
>> the box is cubic and about an order of magnitude larger in each
>> dimension than an "average" system.
>>
>> -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
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>



-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*