Pan Wu wrote:
Hi everyone,
Thank you for answering my former questions, it really help me, the
new gmx-er a lot~
Here is another question about reference state of RMSF.
In the manual, it shows "g_rmsf computes the root mean square
fluctuation (RMSF, i.e. standard deviation) of atomic positions
after (optionally) fitting to a reference frame". So in this way, can I
choose the reference frame from *.tpr file or the coordinate average
over the whole trajectory? If Gromacs can, how?
I believe the reference structure is taken from whatever structure file is given
to the -s flag, so in principle you could provide any frame from the trajectory,
as well as the initial one, or some average structure (from, i.e. g_cluster or
something similar).
-Justin
Thank you in advance!
--
Sincerely
=================================
Pan Wu
Graduate Student in Department of Chemistry
Duke University
124 Science Drive
5301 French Family Science Center
Durham, NC 27708
Phone: (919) 660-1583
=================================
------------------------------------------------------------------------
_______________________________________________
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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
