[gmx-users] RMSF problem

[Mark Abraham]

Also, knowing the group you selected in the mdp for writing the xtc file is
key to understanding why what you get might not match what you are trying
to do...

Mark

On Fri, May 12, 2017 at 1:51 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/11/17 1:43 PM, Franco Henrique wrote:
> > Dear Justin Lemkul,
> >
> > Thank’s for prompt reply.
> >
> > My protein has 198 aminoacides (PDB: 2GOJ;
> http://www.rcsb.org/pdb/explore.do?structureId=2GOJ). After RMSF command
> (gmx rmsf -f .xtc -s .tpr -o .xvg -res), the output has only 103
> aminoacides as visualized by Grace software. I am running gromacs 5.1.2 in
> ubuntu.
> >
> > Any inquiries are more than welcome.
> >
>
> Your full screen output and an upload of the output file (to a file-sharing
> service, as the list does not accept attachments) would be helpful.
> There's no
> logical reason for gmx rmsf to randomly ignore residues.  Did you
> simulate/analyze the whole dimer structure, or just one chain?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.