[gmx-users] Which .tpr file to use for g_rms?
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Dec 4 09:45:21 CET 2010
On 4/12/2010 6:45 PM, Anirban Ghosh wrote:
> Thanks a lot for the reply.
> But I am getting different results with the two .tpr files (first and
> last) using the following commands:
>
> trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 10000 -pbc nojump
> trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 10000 -pbc nojump
Did you read trjconv -h about -pbc nojump? Notice how when you didn't
give your command lines last time, you didn't get a very useful answer.
> So which .tpr file should I use?
You're trying to measure a membrane thickness. So you want all the
membrane residues in the same box, and don't care about anything else.
There's various ways to use -pbc and -center to achieve this, depending
on what the simulation has done.
Mark
>
> Thanks,
>
> Anirban
>
> On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> On 4/12/2010 4:33 PM, Anirban Ghosh wrote:
>
> Thanks a lot for the reply.
> Actually I am running a protein in lipid bilayer. Now I want to
> calculate the thickness of the bilayer at the end of the
> simulation.
> So for that I want the last structure (.gro) file. So I am
> trying to
> dump the last structure using trjconv (with -pbc option). So to do
> this which .tpr file should I supply to trjconv, the first one
> or the
> last one?
>
>
> Since you're not using the coordinates in the .tpr file to extract
> the last frame and map its coordinates onto the .tpr's atom names,
> it can't matter what they are.
>
> Mark
>
>
> Thanks again.
>
> Anirban
>
> On 12/4/10, Justin A. Lemkul<jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
> Anirban Ghosh wrote:
>
> Thanks a lot Justin for the reply. Yes, I understand
> that. But ideally
> which structure should be used as the reference, in a
> general, the
> starting structure or the end structure?
>
> That's up to you to decide based on what you need to
> measure. Do you want
> the
> RMSD relative to your starting (i.e. crystal/NMR)
> structure, or are you
> trying
> to study how a protein folds, in which case you'd use the
> native (end)
> state?
>
> like when I an using trjconv to dump my last frame
> (with "-pbc nojump"),
> which .tpr file should I use to get the exact picture
> of what has
> happened to my protein at the end of the simulation.
> Should I use the
> first .tpr file or the last .tpr file?
>
> I don't understand what you mean. "What has happened" is
> an entire
> trajectory,
> not a snapshot.
>
> -Justin
>
> Thanks a lot again.
>
> Anirban
>
> On Fri, Dec 3, 2010 at 7:35 PM, Justin A.
> Lemkul<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Anirban Ghosh wrote:
>
> Hi ALL,
>
> Its a very basic question but still...
> When we calculate RMSD (or any other
> parameter) using the g_rms
> command, we need to supply the .tpr file with
> -s option. Now
> suppose if I have a total 20 ns simulation
> with 4 breaks (i.e 5
> ns in each run), then there will be 4 .tpr
> files. So at the end
> of 20 ns if I wish to calculate RMSD, then
> which .tpr file
> should I suppy to g_rms, the first one or the
> last one? We I run
> g_rms with the two .tpr files, I get different
> results. So which
> one should be used? Any suggestion is welcome.
>
>
> Use the one that contains the structure you wish
> to serve as your
> reference.
>
> -Justin
>
>
> Thanks,
>
> Anirban
>
>
> --
> ========================================
>
> 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><http://vt.edu>
> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search
> before posting!
> Please don't post (un)subscribe requests to the
> list. Use the www
> interface or send it to
> gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> ========================================
>
> 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
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101204/df8238dd/attachment.html>
More information about the gromacs.org_gmx-users
mailing list