Hi,
I am trying to extract snapshots and center on a particular group, but the
center of the box does not correspond to the geometric center of the group
as expected. It is centered on the outer edge of the group. Here is the
command I am using:
gmx trjconv -f md.xtc -o md_201000ps.pdb -s md.tp
Hi again,
As a follow up to my earlier email -- I added -pbc atom to the flags, for a
total command line of:
gmx trjconv -f md.xtc -o md_201000ps.pdb -s md.tpr -b 201000 -e 201000 -n
INDEX.ndx -pbc atom -center
This brought it "closer" to the group I chose being centered, but it is
still not cen
Hi,
I also had that experience with trjconv with various versions. I ended up
doing the centering by a script.
I know on the other hand that centering works well in the case of for
example gmx density. Yet I've had no luck with trjconv...
Maybe this is known issue..?
Regards,
Gyorgy
On Tue, 5 Fe
Hi,
It would be helpful to know if this is a known bug/issue. I'd rather not
have to write code to recenter in this case -- would be easy if I just had
one molecule far from the edges of the box but I am simulating a crowded
system and need to get it centered on one complex within the system whil
...and as a follow up, it doesn't seem to be centering at either the
geometric center OR the center of mass. Any insight would be appreciated.
Mala
On Wed, Feb 6, 2019 at 10:15 AM Mala L Radhakrishnan
wrote:
> Hi,
>
> It would be helpful to know if this is a known bug/issue. I'd rather not
>
Hi,
There are a few issues related to gmx trjconv -center:
a)
http://redmine.gromacs.org/projects/redmine-platform/search?all_words=1&attachments=0&commit=Submit&issues=1&options=0&page=1&q=-center&scope=all&titles_only=&utf8=%E2%9C%93
b) http://redmine.gromacs.org/issues/2579
but not sure if
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
ma
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 bo
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.
thanks again for
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 o
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
Hi Mala,
Please combine -center with "-pbc mol -ur compact" and check.
Regards,
Rajat
--
Dr. Rajat Desikan
Invictus Oncology, Delhi
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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What does "gmx energy -b 2 -e 2" 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
Hi Paul,
Thanks for this idea --
...But it returns what I would expect:
Statistics over 1 steps [ 20. through 20. ps ], 3 data sets
All statistics are over 1 points
Energy Average Err.Est. RMSD Tot-Drift
-
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 [ 20. through 20. ps ], 3 data sets
All statistics are over 1 points
Energy Average Err.Est. RMSD Tot
On 2/8/19 5:17 AM, Rajat Desikan wrote:
Hi Mala,
Please combine -center with "-pbc mol -ur compact" and check.
Compact unit cell representation is only useful for dodecahedral and
octahedral boxes. A cubic box is already as compact as it can be.
-Justin
--
===
Hi Justin,
"A cubic box is already as compact as it can be."
That's true and I understand that :) it's just that I have faced similar
issues with trjconv that Mala appears to be grappling with, and this
combination has always resolves it for me. I don't know why. I can attach
test files that show t
On 2/8/19 7:22 AM, Rajat Desikan wrote:
Hi Justin,
"A cubic box is already as compact as it can be."
That's true and I understand that :) it's just that I have faced similar
issues with trjconv that Mala appears to be grappling with, and this
combination has always resolves it for me. I don't
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 necess
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 a
Hi Rajat,
Thanks -- but I don't want -pbc mol because that keeps my molecules whole,
which I don't want. I actually want to keep the shape of the cubic box for
my purposes. Maybe I'll try -pbc atom -ur compact, but I think I tried that
and it didn't work -- but will try again.
Mala
On Fri, Feb
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?
Thanks again so much
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
Hi Justin,
Yes, but I don't want anything sticking out of the box. I need the shape
of my entire system, when visualized, to be wholly contained within the
cubic shape -- and centered on the desired group. That's pretty much all.
Does this clarify? Does this change what you recommend?
Mala
On 2/8/19 8:29 AM, Mala L Radhakrishnan wrote:
Hi Justin,
Yes, but I don't want anything sticking out of the box. I need the shape
of my entire system, when visualized, to be wholly contained within the
cubic shape -- and centered on the desired group. That's pretty much all.
Does this c
...and molecules at the edges can totally be broken. So really just a
translation of the box coordinates to be centered on the desired group. It
should really be very straighforward.
If it's easier to take offline, I'm happy to.
M
On Fri, Feb 8, 2019 at 8:29 AM Mala L Radhakrishnan
wrote:
>
ok -- thanks -- am to trying this out now.btw, I am also running 2016.3
to analyze a trajectory made with 2016.4. I tried a couple of versions
and still got the same weird behavior, but I thought I'd let you know in
case you know that using a slightly older version to analyze a newer one is
p
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