On 2/8/19 6:52 AM, Mala L Radhakrishnan wrote:
Hi Paul,
Thanks for this idea --
...But it returns what I would expect:
Statistics over 1 steps [ 200000.0000 through 200000.0000 ps ], 3 data sets
All statistics are over 1 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Box-X 12.2482 -- 0 0 (nm)
Box-Y 12.2482 -- 0 0 (nm)
Box-Z 12.2482 -- 0 0 (nm)
This matches what the pdb extracted file says (i.e. the file which does not
have the complex centered at the Box-X/2, Box-Y/x, Box-Z/2)
So I'm still not sure what's going on -- any other thoughts?
From your trjconv command, it looks like you are somewhat inefficiently
trying to simply output the final frame, is that correct?
I have found quirky behavior in trjconv when trying to do multiple
actions (you're centering and manipulating PBC at the same time) while
also skipping many frames. Here's what I would suggest:
gmx trjconv -s md.tpr -f md.xtc -pbc mol -o md_mol.xtc
gmx trjconv -s md.tpr -f md_mol.xtc -center -o md_center.xtc -n index.ndx
gmx trjconv -s md.tpr -f md_center.xtc -dump 200000
Does that improve the situation? If not, please send a minimal test case
to me off-list and I will take a look.
-Justin
Mala
On Fri, Feb 8, 2019 at 5:39 AM Peter Kroon <p.c.kr...@rug.nl> wrote:
What does "gmx energy -b 20000 -e 20000" give as box dimensions?
Peter
On 07-02-19 22:20, Mala L Radhakrishnan wrote:
Hi Justin,
Thank you -- the good news is that the center of mass of this group does
in
fact match what I calculate to be the COM with my script.
BUT, the bad news is that this is not in the center of the box after I
have
asked for it to be centered (which I presume it should be)::
COM:
5.95324 6.00572 5.68943
The cubic box is 12.249 long (as noted in the CRYST1 field of the pdb
file
and its left corner is at the origin (I know this because I have atoms
that
go all the way to the edges of the box and my minimum x,y, and x
coordinates are basically 0 and my maximum are basically 12.24 in all
three
directions, which would make the center of the box:
6.1245, 6.1245, 6.1245
So it's close but a few angstroms off. Can you please tell me what might
be going on here? I am happy to share files with, as I'd be really
grateful for your help. Again, I've written a scrip to translate and
"wrap" the atoms across the pbc in the worst case scenario, but I have to
imagine gromacs should be able to do this correctly.
Again - this is the command I used to extract the hopefully centered
frame:
gmx trjconv -f md.xtc -o all.pdb -s md.tpr -b 200000 -e 200000 -n
INDEX.ndx
-pbc atom -center
...and I chose the correct index (and extracted the same atoms just in
case
to make sure that I knew exactly what atoms it thought it was centering,
in
case something was in fact wrong with the index file)
Thank you so much,
Mala
On Thu, Feb 7, 2019 at 1:54 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 2/7/19 1:52 PM, Mala L Radhakrishnan wrote:
Hi Justin,
I've verified the I'm entering in the right group and that it's correct
in
the index file. Where do I find the output for what it thinks is the
center of mass before and after? That would be helpful output, but I
haven't found such output in standard output or error.
gmx traj -ox -com
-Justin
thanks again for instructions on how to get this info..
Mala
On Thu, Feb 7, 2019 at 1:46 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 2/7/19 1:36 PM, Mala L Radhakrishnan wrote:
Thanks...but these don't really address the issue I have. I've
written
my
own script now to do re-centering and looping of atoms across the box
walls
myself, but I am still really unclear why -center does not in fact
center
the molecule in the box either at its geometric center OR its center
of
mass (I have written scripts to test both out and neither match, and
visually the molecule is clearly not centered in the box)
To me it definitely seems like something is not right with this
utility
or
something about the options I've used are conflicting in ways I don't
understand:
-pbc atom -center (a group from index file)
Thanks again for any other ideas...
I've only been loosely following this thread, but I've never had a
problem where trjconv didn't center as I wanted. Have you verified
that
the index group is correct, and you're making the proper selection?
What
does gmx traj report as the center-of-mass coordinates for those
groups
before and after trjconv tries to center them?
-Justin
--
==================================================
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.
--
==================================================
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.
--
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.
