Hi Daniel
Thanks
>>
Have you tried using other molecules as the 'anchor' molecule? For example:
I tried different, autoimage anchor :
and molecule looks fine and not 'broken' and is in the box "but" not in the centre of box, which I think not an issue because as you said imaging for visualization and analysis (rdf, distance) are different algorithms. My molecule does not have any central sort of residue as its empty from inside so changing different anchors, I believe, wont have much affect.
(Also I think if molecule goes out of box in visual imaging it should not have any issues as its a PBC?)
I was in
wrong impression that it was a sort of autoimaged trajectory which is used for analysis of RDF, distance etc. (what we see is analysed as well!). I would be much
thankful if you can please can refer to some paper/link which explains the
pseudo algorithm and difference between these two image processes.
Just for info: I just checked my initial polymer max. length was 137 Angs (and I used 12 Angs water shell) which now reduced to 125 approx.
thanks
J
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>
> I tried to see restart file generated using cpptraj its same. Broken I
> mean to say : the broken part is on the opposite side of box so just image
> periodicity issue
>
Have you tried using other molecules as the 'anchor' molecule? For example:
autoimage anchor :253-269
As I said before, cpptraj by default uses the first molecule as the anchor,
but if that molecule is not 'central' to all other solute molecules then
autoimage may not work as expected. If you want, send me (off-list)
topology/restart files (or even a mol2) and I can make a more specific
recommendation.
> >> No worries here - unless you specify 'noimage' to 'radial', imaging is
> done for you
>
> So I dont need to do image traj first and then do RDF analysis? Also
> imaging is done by default for other analysis as well, like distance etc.?
>
No, as I said the 'radial' command images distances by default. The
'distance' command does as well unless 'noimage' is specified. The manual
states whether a command performs imaging by default or not so I recommend
you read the manual carefully. For example, the 'hbond' command does not
perform imaging.
>
> But what kind of imaging done by default? As I see autoimage if I do
> manually it does not work and even if it works my molecule is not in center
> of box
>
Re-imaging for visualization and imaging distances are two different
procedures. When re-imaging for visualization (e.g. the autoimage command)
you are re-centering the trajectory on a molecule of interest, then
re-imaging everything that may now be outside the unit cell back into the
unit cell. It doesn't always work because autoimage is essentially trying
to guess what the final picture should look like. Imaging distances (e.g.
the distance command) is a more basic procedure; you are just trying to
find the shortest distance between two points in periodic space, which
*always* works. So even if the visualization looks 'broken', imaging is
always done correctly internally so the 'radial' command will work just
fine.
Hope this helps,
On Thursday, January 23, 2014 5:47 PM, Jio M <jiomm.yahoo.com> wrote:
Hi Daniel
>> What are your box dimensions?
starting box dimensions: 154.4068135 154.4068135 154.4068135
taken from restart file after 72 ns: 149.0627735 149.0627735 149.0627735
>> Since PDB files don't have bond information VMD has to guess where the bonds
are, which can lead to things looking >>broken. Either use the prmtop with the PDB in VMD or better yet write a mol2 file (which has bond info).
trajin temp.nc
autoimage
trajout temp.rst restart
I tried to see restart file generated using cpptraj its same. Broken I mean to say : the broken part is on the opposite side of box so just image periodicity issue
>> Without knowing more details about your system (is there one 'solute' molecule or multiple?
It has 10 molecules (TER card separated)
>> No worries here - unless you specify 'noimage' to 'radial', imaging is done for you
So I dont need to do image traj first and then do RDF analysis? Also imaging is done by default for other analysis as well, like distance etc.?
But what kind of imaging done by default? As I see autoimage if I do manually it does not work and even if it works my molecule is not in center of box
Thanks
On Thursday, January 23, 2014 4:39 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
Hi,
On Thu, Jan 23, 2014 at 9:06 AM, Jio M <jiomm.yahoo.com> wrote:
I have a linear long molecule around 120 angs and am using truncated octahedron water box.
>
What are your box dimensions?
I am trying to test imaging on single restart file with cpptraj (for analysis of traj files for RMS mass weighted and radial distrubution of ions.)
>
>When I use:
>
>trajin test.nc
>autoimage
>trajout test.pdb pdb
>
>My linear molecule is out of box partially and looks "broken"! (but it is not broken if I just check the rst and prmtop in vmd)
>
Since PDB files don't have bond information VMD has to guess where the bonds are, which can lead to things looking broken. Either use the prmtop with the PDB in VMD or better yet write a mol2 file (which has bond info).
I tried:
>trajin test.nc
>autoimage :253-269
>trajout test.pdb pdb
>
>
>253-269 are residues in one molecule and it shows nice unbroken structure though whole structure does not look (visually in vmd) in
>
Without knowing more details about your system (is there one 'solute' molecule or multiple?) it's tough to comment here. In general, for autoimage to work properly you should pick as the 'anchor' molecule the molecule that has the shortest distance to all other 'fixed' molecules; autoimage by default assumes the first molecule should be used as the 'anchor'.
>1) What image processing should be done for RDF calculations and ofcourse I can use same traj for RMS analysis. I mean the molecule should be in center if RDF analysis to be done correcly.
>
No worries here - unless you specify 'noimage' to 'radial', imaging is done for you.
>2) Also as in ptraj I did not find 'mass' flag with cpptraj for rms calculations? can it be used in cpptraj as in ptraj
>
The 'mass' keyword has always been supported in the 'rms' command in cpptraj (see the manual or internal help).
>3) In section 8.9, Page number 230 AmberTools13 manual, the 'rmsd' and 'rms' are different things?
>
They are the same command; 'rms' is supported for backwards compatibility.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jan 23 2014 - 10:30:04 PST
