[gmx-users] trjconv pbc options

[RINU KHATTRI]

hello  Tsjerk Wassenaar
can we use both command pbc whole and pbc nojump and in which stage of
 simulation we have to use it because in the tutorial it  is written
before center the protein in the box
thanks in advance

On Thu, Sep 18, 2014 at 9:40 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Prathiba,
>
> With -pbc nojump, an atom that jumps from one side to the box to the other
> is reset, so the trajectory is made continuous. If the molecule is broken
> and you remove jumps, the molecule will stay broken.
>
> With -pbc whole, the molecule is made whole, which means that the atoms are
> shifted such that all bonds have the correct lengths. The algorithm starts
> with the first atom of the molecule, so if that atom jumps over PBC, then
> -pbc whole will make the whole molecule jump.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Sep 18, 2014 at 5:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/18/14 11:51 AM, pratibha kapoor wrote:
>>
>>> Hi users
>>>
>>> I have question regarding difference between pbc whole and pbc nojump
>>> options using trjconv. Please help me understand this.
>>>
>>>
>> Have you read trjconv -h yet?
>>
>> -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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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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