[gmx-users] pbc whole
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Feb 17 15:18:04 CET 2010
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
>> >>>
>> >>> ========================================
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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
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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>
>
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--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
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