[gmx-users] trjconv pbc options

[Tsjerk Wassenaar]

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
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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-- 
Tsjerk A. Wassenaar, Ph.D.