[gmx-users] pbc whole

Carla Jamous carlajamous at gmail.com
Wed Feb 17 15:22:59 CET 2010 

Thank you sooo much Tsjerk,
I've been struggling for 3 days to understand how g_rmsf works.
Thank you, your explanation is very clear.

Cheers,
Carla

On Wed, Feb 17, 2010 at 3:18 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Carla,
>
> What g_rmsf does is calculate the first (average) and second
> (fluctuation) central moments. For that, it is required that the
> conformational space is defined, which is done by fitting each frame
> to the reference structure. The reference is only used for that. The
> fluctuation is calculated about the mean position. It doesn't make
> sense to most people to calculate a non-central second moment, so be
> assured that that's not what g_rmsf does (for the few people
> interested, it can be  done with g_covar :p).
>
> g_rmsf does what you want.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Feb 17, 2010 at 3:06 PM, Carla Jamous <carlajamous at gmail.com>
> wrote:
> > Thank you Tsjerk,
> > but one more question:
> > if I do the following: g_rmsf -f a.xtc -s b.tpr -o rmsf.xvg -ox
> average.pdb
> > -n c.ndx
> >
> > does gromacs claculate the rmsf after fitting to b.tpr or to average.pdb?
> > & if I want it to calculatefluctuations between the position of
> > particle i and the time-averaged position of the same particle i, do I
> have
> > to do:
> >
> > g_rmsf -f a.xtc -s average.pdb -o rmsf.xvg?????
> >
> > Thank you & sorry to bother. I'm just trying to understand what g_rmsf
> > really does, to help me analyze my results.
> >
> > Carla
> >
> > On Wed, Feb 17, 2010 at 10:25 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> > wrote:
> >>
> >> Hi Carla,
> >>
> >> Justin's recipe should've worked. As he suggested, maybe the ligand is
> >> not with the protein. You can check by multiplying your system with
> >> genconf:
> >>
> >> genconf -f in.pdb -o out.pdb -nbox 2 2 2
> >>
> >> If the ligand is with the protein, one copy will be located in one of
> >> the copies of the protein.
> >>
> >> g_rmsf does write the average structure, if requested. Use the option
> -ox
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >> On Wed, Feb 17, 2010 at 10:08 AM, Carla Jamous <carlajamous at gmail.com>
> >> wrote:
> >> > Hi Justin,
> >> > I'm still trying to figure out what happened with my ligand.
> >> > Meanwhile, I have another question: I can't figure out how to
> calculate
> >> > an
> >> > average structure in gromacs.
> >> > And does g_rmsf calculate the average structure automatically?
> >> >
> >> > Thanks again
> >> > Carla
> >> >
> >> > On Tue, Feb 16, 2010 at 5:44 PM, Justin A. Lemkul <jalemkul at vt.edu>
> >> > wrote:
> >> >>
> >> >>
> >> >> Carla Jamous wrote:
> >> >>>
> >> >>> Hi Justin,
> >> >>> Thank you for your answer but I'm still not getting my ligand to
> stay
> >> >>> in
> >> >>> the box.
> >> >>>
> >> >>> I tried the following(after taking a look at the mailing list
> >> >>> archive):
> >> >>>
> >> >>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol
> >> >>> (centering on "Protein")
> >> >>> trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans
> >> >>>
> >> >>> So please do you have another advise to give me?
> >> >>>
> >> >>
> >> >> If that's not working, then I wonder if your ligand is still actually
> >> >> bound to your protein :)  The above sequence always works for me, as
> >> >> long as
> >> >> there actually is a complex.  You can also try -pbc cluster, but I
> know
> >> >> that
> >> >> algorithm can hang.
> >> >>
> >> >> -Justin
> >> >>
> >> >>> Thanks
> >> >>> Carla
> >> >>>
> >> >>> On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu
> >> >>> <mailto:jalemkul at vt.edu>> wrote:
> >> >>>
> >> >>>
> >> >>>
> >> >>>    Carla Jamous wrote:
> >> >>>
> >> >>>        Hi everyone,
> >> >>>        I'm using this command to extract my protein and my ligand
> from
> >> >>>        the trajectory.
> >> >>>
> >> >>>        trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans
> -pbc
> >> >>>        whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >&
> outtrj
> >> >>>
> >> >>>        Before, I had a problem with residues of my protein showing
> at
> >> >>>        the other end of the box, when I display my .xtc with VMD.
> >> >>>        the "-pbc whole" fixed it.
> >> >>>
> >> >>>        However, now I have another issue: my ligand is at the other
> >> >>> end
> >> >>>        of the box. So please can anyone tell me what can I do to fix
> >> >>>        that and get a reasonable RMSD value?
> >> >>>
> >> >>>
> >> >>>    You may need several more iterations of trjconv (one rarely does
> >> >>> the
> >> >>>    trick), employing -pbc nojump, -pbc cluster, and/or -center.  For
> >> >>>    protein-ligand complexes, I have often found that the combination
> >> >>> of:
> >> >>>
> >> >>>    trjconv -pbc mol -ur compact -center
> >> >>>
> >> >>>    (centering on "Protein")
> >> >>>
> >> >>>    does the trick.  And it makes molecules whole, as well :)  I
> think
> >> >>>    there are also some breakdowns (documented somewhere in the list
> >> >>>    archive) when applying -fit and -pbc in the same step.  I believe
> >> >>> it
> >> >>>    is recommended to fix PBC first, then applying any sort of
> fitting
> >> >>>    in a separate, subsequent step.
> >> >>>
> >> >>>    -Justin
> >> >>>
> >> >>>        Thank you
> >> >>>        Carla
> >> >>>
> >> >>>
> >> >>>    --    ========================================
> >> >>>
> >> >>>    Justin A. Lemkul
> >> >>>    Ph.D. Candidate
> >> >>>    ICTAS Doctoral Scholar
> >> >>>    MILES-IGERT Trainee
> >> >>>    Department of Biochemistry
> >> >>>    Virginia Tech
> >> >>>    Blacksburg, VA
> >> >>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> >> >>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >> >>>
> >> >>>    ========================================
> >> >>>    --    gmx-users mailing list    gmx-users at gromacs.org
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> >> >>>
> >> >>>
> >> >>
> >> >> --
> >> >> ========================================
> >> >>
> >> >> Justin A. Lemkul
> >> >> Ph.D. Candidate
> >> >> ICTAS Doctoral Scholar
> >> >> MILES-IGERT Trainee
> >> >> Department of Biochemistry
> >> >> Virginia Tech
> >> >> Blacksburg, VA
> >> >> jalemkul[at]vt.edu | (540) 231-9080
> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >> >>
> >> >> ========================================
> >> >> --
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> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> Computational Chemist
> >> Medicinal Chemist
> >> Neuropharmacologist
> >> --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
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