Sorry but the help does not help me... In anycase, the help of
g_rmsdist say: "g_rmsdist computes the root mean square deviation of
atom distances, which
has the advantage that no fit is needed like in standard RMS deviation as
computed by g_rms..."; so no fit is needed, for me it means that there
is no superimposition... Can you explain me where I'm wrong?
Valerio
Tsjerk Wassenaar <tsje...@gmail.com> ha scritto:
Hi Valerio,
Check the help for both tools. That explains it all.
Oh, and you're not correct ;)
Cheers,
Tsjerk
On Mon, Dec 5, 2011 at 4:42 PM, <vferra...@units.it> wrote:
Dear all,
I need to calculate the RMSD of a protein during time. So that I've
calculated the trajectory; for the calculation which tool should I use?
g_rms or g_rmsdist ? Which is the difference between these two tools? If I'm
right the main difference is that with g_rms the structure at the time t is
superimposed to the reference structure before calculate the RMSD, while
with g_rmsdist the RMSD is calculated without any superimposition, am I
correct?
Valerio
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
--
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/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use thewww interface
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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/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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
--
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/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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
