[gmx-users] Question regarding box size

Justin Lemkul jalemkul at vt.edu
Fri Jul 10 23:13:08 CEST 2015

On 7/10/15 1:35 AM, James Lord wrote:
> Hi all,
> I have a system with 300k atoms, but computationally it is expensive for me
> doing simulation with such a big system, Is it possible to reduce the box
> size? If yes how? (the .gro file is uploaded). I know from Justin tutorial
> genconf
> -nbox        vector 1 1 1
> Does the numbers after -nbox have to  integer?
> The size of box required to contain protein with 1.5nm of water on each
> side. Sorry I could not figure it out what to do and how to tackle this
> simple task. re bulding the simulation from scratch is an option but
> thought might find quicker and smarter way here. I want to have optimum
> size in each direction so that the protein does not see its periodic image.
> Appreciate any specific thoughts on my system and the box size I have got
> now.
> https://drive.google.com/file/d/0B0YMTXH1gmQsdFVKWkdPLURCUVk/view?usp=sharing

Given that you have a large protein and you're creating a biphasic system, 
there's not much you can do.  The water box may be a bit large along z, but 
that's about all you can likely change here.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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