On 2/8/19 8:15 AM, Mala L Radhakrishnan wrote:
Hi Justin,
Also -- this is important, I need to maintain the shape of the cubic box,
so I do *not* want to keep molecules at the box edges whole (I know this
sounds weird, but I need it for my applications) -- so should I use -pbc
atom instead of -pbc mol for the first step?
The shape of the box will not change with any of the -pbc options, you
may just have a few atoms sticking "out" of the actual dimensions
depending on PBC treatment. But the *box* never changes unless you
re-wrap or manipulate it with -ur (though, as I've said for a cube, you
can't really actually change).
-Justin
Thanks again so much -- just want to make sure before I start making these
huge files :)
Mala
On Fri, Feb 8, 2019 at 8:07 AM Justin Lemkul <jalem...@vt.edu> wrote:
On 2/8/19 8:03 AM, Mala L Radhakrishnan wrote:
Hi Justin,
Thank you SO much -- I will try this out, but I have a silly question
before I do -- is there a way to dump just the desired frame in the first
step itself -- or would that screw up the ordering -- since my xtc files
are just so huge and I'd rather not create more huge files than
necessary?
If there is no other way, then I will do it, but these are massive files
and I'd need to create them for many simulations.
You can try, but my suggestion is that you have to be careful in making
leaps from one reference state to a final state. In principle, it should
work no matter what, but I've noticed that trjconv does sometimes
require processing of a full trajectory for PBC and fitting purposes. I
have no explanation as to why, but if you carefully and methodically
invoke trjconv, there should never be a problem getting it to behave as
you need it to.
-Justin
Thanks,
M
On Fri, Feb 8, 2019 at 6:56 AM Justin Lemkul <jalem...@vt.edu> wrote:
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
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Lab: 303 Engel Hall
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Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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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
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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
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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
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