[gmx-users] pbc problem

[Mark Abraham]

On Sun, Feb 2, 2014 at 5:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/2/14, 7:15 AM, Atila Petrosian wrote:
>
>> Dear Justin and Tsjerk
>>
>> you said " Some tools handle PBC properly, some don't ".
>>
>> I want to know exactly which tools of gromacs handle PBC properly.
>>
>> Can I find these tools in manual?
>>
>>
> No, because it's not possible to test every single command that the user
> might issue and keep a reliable database of such information.


True, but there is some partial information available - see e.g. known
problems under genbox -h. It would certainly be a Herculean task to curate
testing, documentation and/or fixing all such issues, though!

Mark


>
>  I did simulation of a system containing protein and cnt using gromacs
>> 4.5.6.
>>
>> When I see trajectory by VMD, in some frames, protein atoms exit one side
>> of box
>> and enter opposite side of box. I want to do analysis of trajectory. I do
>> not know
>> exactly this state is pbc problem or not.
>>
>>
> Again, that depends entirely upon the command you're using.  Tools like
> g_rms have problems when molecules are split across PBC.  Other tools like
> g_dist or g_msd handle the situation better.  If the protein is the only
> problematic molecule, it should be rather trivial to fix the PBC issues
> with trjconv -center, trjconv -pbc nojump, trjconv -pbc mol -ur compact, or
> trjconv -fit translation, or perhaps some sequence of those.  Please refer
> to the PBC link I have posted several times this week.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> 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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