[gmx-users] Erro in SMD simulation..

[Justin Lemkul]

On 4/1/14, 12:56 PM, Kalyanashis wrote:
> Thank you Justin for your valuable reply. But you know, my box size is
> 17.744*17.744*17.744 nm^3. I have used "editconf -bt cubic -f
> 20-SCH-edit1.pdb -o 20-SCH-edit2.pdb -c -d 1.6" to generate the box.  And
> the full description of the box size I have used is
> "Read 15484 atoms
> No velocities found
>      system size :  7.604  8.101 13.546 (nm)
>      diameter      : 14.544               (nm)
>      center         :  2.405  3.212 -2.870 (nm)
>      box vectors  :  0.000  0.000  0.000 (nm)
>      box angles   :   0.00   0.00   0.00 (degrees)
>      box volume  :   0.00               (nm^3)
>      shift             :  6.467  5.661 11.742 (nm)
> new center       :  8.872  8.872  8.872 (nm)
> new box vectors : 17.744 17.744 17.744 (nm)
> new box angles  :  90.00  90.00  90.00 (degrees)
> new box volume  :5587.13               (nm^3)"
> Please suggest me the better option for my system. Should I increase the d
> value? Actually, the whole system contains approximately 193000 atoms and
> whenever I am increasing the d value the atoms no. is increasing
> significantly. Is there any option which can allow me to increase the box
> size without increasing the number of solvent molecules?  And one more more
> thing, is the cubic option fine?

You're using pressure coupling so the box vectors change over time.  The error 
complains because 8.662854 * 2 = 17.325708, which is totally feasible to expect 
for normal box vector fluctuations.

A cubic box is usually the most inefficient shape for most systems.  Depending 
on the symmetry of your system, you can probably do a lot better.  If you're 
pulling only along z, then a rectangular box with a suitable z-dimension is 
probably the next easiest way to go and will save you a ton of unnecessary water 
molecules.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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