[gmx-users] problem with protein secondary structure analysis
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 17 12:43:36 CEST 2008
Alright, so this is from your NVT run then, but what about NPT? I'm guessing
somewhere along the line you introduced options regarding the .xtc file (I don't
see nstxtcout or xtc-grps here). But then that's inconsistent with what you've
told us about what's in your trajectory! Be very careful that you know what
you've assembled in the .xtc file, because from the .mdp file you've shown, no
.xtc file will be written, even though you say you've got one.
See what gmxcheck tells you about your .xtc file regarding number of frames and
number of atoms. This will tell you if something is missing, or if something
you do not expect is actually in the .xtc file.
Certainly a lesson in being careful... :)
> Sorry for the mistake Tsjerk
> I havent comment on xtc-grps in .mdp file for confirmation pasting .mdp file
> title = dpt_prod
> constraints = hbonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 3000000 ; total 250 ps.
> nstcomm = 1
> nstxout = 100
> nstlog = 100
> nstenergy = 100
> nstlist = 10
> ns_type = grid
> coulombtype = PME
> rlist = 0.9
> rcoulomb = 0.9
> rvdw = 1.4
> pbc = xyz
> comm_grps = Protein
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = Berendsen
> tc-grps = Protein SoL_CL-
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; isotropic pressure coupling is off
> Pcoupl = no
> pcoupltype = isotropic
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> Couls you please tell me how can I select subset of my trajectory file.
> May be this is simple question.
> Thanks in advance.
> Hi Minnale,
> We do appreciate that english is not your native language (it isn't
> mine either), but please try to write correct, complete sentences.
> That will make it easier to read your posts, understand what you did
> and where you went wrong and how we can, maybe, provide you a
> Justins reply was right on, and you didn't read his post carefully
> enough. He said to check your xtc-grps, not your tc-grps. xtc-grps, as
> it is unambiguously explained in the manual, determines which sets of
> atoms are saved to the .xtc file. To avoid such confusion, make it a
> habit to paste the .mdp file when you post a problem (after having
> checked the manual, the wiki, and the archives of the list, that is).
> On Sun, Aug 17, 2008 at 7:30 AM, minnale <minnale_gnos at
> rediffmail.com> wrote:
> > Thanks to Justin for his prompt reply
> > in .mdp file mentioned energy groups and tc-grps are protein and
> sol_cl . I
> > am in doubt that first 250ps of md run it in npt condition later nvt till
> > 7ns finally made into long .xtc file.
> > I tried your suggested way in earlier post but I didnt get it.
> > one more doubt I am having is
> > If I load entire .xtc file which contain 7ns trajectory it didnt load
> > Could please tell me why its not loading
> > Thanks in advance.
> On Sat, 16 Aug 2008 Justin A.Lemkul wrote :
> >minnale wrote:
> >> Hi all,
> >> I intersted in analysing secondary structure of protein by using
> VMD and performed these steps.
> >>1. First loaded min.gro file and corresponding min.xtc then all
> equalibration .xtc files till here MD movie has run fine.
> >>2. I had long trajectory in a single file, so cut it down into
> subtrajectories with 1ns interval by using *trjconv command and issued
> like this
> >> trjconv -f .xtc -o 1ns.xtc -s .tpr -b 0 -e 1000
> >> selected system, it showed
> >>Fatal error:
> >>Index 2726 is larger than the number of atoms in the trajectory
> file (2725)
> >You've only saved a subset of your trajectory. Check the xtc-grps in
> your .mdp file. You can use trjconv if you have a reference structure
> that matches the contents of your trajectory.
> >>Could you please give me suggestion if any one have experienced this
> type of problem
> >>Thanks in advance.
> >>Rediff Shopping
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> >-- ========================================
> >Justin A. Lemkul
> >Graduate Research Assistant
> >Department of Biochemistry
> >Virginia Tech
> >Blacksburg, VA
> >jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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