[gmx-users] Question regarding box size

[James Lord]

Thanks Justin and Victor

On Sat, Jul 11, 2015 at 9:12 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

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