[gmx-users] Nonsymetric molecule across pbc

[Steven Neumann]

Thanks a lot!
Can you please give me a hint how to apply umbrella sampling to the system
of 4 nanotubes with pbc across xyz so that they infinite in length in z
coordinate and 2 of them placed with its half to the unit cell copied
across y coordinate...  I want to see PMF minima (equilibrium distance)
between their centre of mass... With 2 nanotubes that would be easy (your
tutorial) but with 4 of them? I am thinking of changing the distance
between and run windows but no clue which group setup as group0 and
group1...

I would appreciate your advise,

Steven




On Tue, Feb 18, 2014 at 5:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/18/14, 11:19 AM, Steven Neumann wrote:
>
>> Dear User,
>>
>> Can you please write me how to build a system of a protein (nonsymetric
>> obviously) and place it in the on the box edge so that one half is within
>> the unit cell and another one is copied across pbc on the other side? I
>> assume I will get the error doing manually...
>>
>>
> Assuming box vectors of length x, y, z:
>
> editconf -center x/2 y/2 z
>
> will split the molecule across the boundary in the positive z-dimension.
>
> I can't think of a situation where this serves any useful purpose that
> centering does not, but that's how you'd do it.
>
> -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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