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 <tsje...@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 <carlajam...@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 <tsje...@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 <carlajam...@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 <jalem...@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 <jalem...@vt.edu > >> >>> <mailto:jalem...@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@gromacs.org > >> >>> <mailto:gmx-users@gromacs.org> > >> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >>> Please search the archive at http://www.gromacs.org/searchbefore > >> >>> posting! > >> >>> Please don't post (un)subscribe requests to the list. Use the www > >> >>> interface or send it to gmx-users-requ...@gromacs.org > >> >>> <mailto:gmx-users-requ...@gromacs.org>. > >> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> >>> > >> >>> > >> >> > >> >> -- > >> >> ======================================== > >> >> > >> >> 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 > >> >> > >> >> ======================================== > >> >> -- > >> >> gmx-users mailing list gmx-users@gromacs.org > >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> Please search the archive at http://www.gromacs.org/search before > >> >> posting! > >> >> Please don't post (un)subscribe requests to the list. Use the www > >> >> interface or send it to gmx-users-requ...@gromacs.org. > >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > >> > > >> > -- > >> > gmx-users mailing list gmx-users@gromacs.org > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > Please search the archive at http://www.gromacs.org/search before > >> > posting! > >> > Please don't post (un)subscribe requests to the list. Use the > >> > www interface or send it to gmx-users-requ...@gromacs.org. > >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > >> > >> > >> > >> -- > >> Tsjerk A. Wassenaar, Ph.D. > >> > >> Computational Chemist > >> Medicinal Chemist > >> Neuropharmacologist > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before > posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > Computational Chemist > Medicinal Chemist > Neuropharmacologist > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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