[gmx-users] pbc whole

Carla Jamous carlajamous at gmail.com
Wed Feb 17 15:06:52 CET 2010 

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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> >
> >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
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