On 3/25/19 2:22 PM, Rituraj Purohit wrote:
Thank you Mark for the reply. In my REMD results I would like to
observe the structure transition with temperature given variation (I
think it is most common observation). My query here is the output of
REMD, It does not give .xtc file but only .edr, .log and .gro
even-thou I indicated -x .xtc during job submission. Is it possible to
perform analysis with .edr, .log & .gro files and without the
Trajectory file? If yes, Please let me know how to do different
analysis such as RMSD, RMSF, Rg etc..
All of those depend on coordinates over time, i.e. the trajectory. Your
existing files cannot be used for such analysis. You will only get an
.xtc file if you specify a non-zero value of nstxout-compressed in the
.mdp file.
-Justin
regards
RajP
On Mon, Mar 25, 2019 at 6:43 PM Mark Abraham <mark.j.abra...@gmail.com> wrote:
Hi,
This is the same as for any other scientific experiment. You need to have
thought about what you hope to learn and what you need to record in order
to analyse the results. REMD is essentially no different here.
Mark
On Sun., 24 Mar. 2019, 10:51 Rituraj Purohit, <riturajpurohi...@gmail.com>
wrote:
Dear Friends,
I performed REMD by following tutorial provided by Mark Abraham, But I
am not able to get the analysis part. Is a step-wise tutorial
available ? I would be thankful to you if anyone of you could help me
to perform analysis of REMD output. Thanking you
Regards
RajP
--
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-requ...@gromacs.org.
--
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-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
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-requ...@gromacs.org.
