[gmx-users] trjconv pbc options

[Tsjerk Wassenaar]

Hi Rinu,

There's a suggested workflow on the Gromacs site. 'nojump' goes before
'center' because the centering may add a shift that messes up the jumps.
'whole' doean't actually change anything, so it can be used anytime before
fitting, which messes up the PBC.

Cheers,

Tsjerk
On Sep 19, 2014 6:26 AM, "RINU KHATTRI" <nickname.mittu at gmail.com> wrote:

> 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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