On 4/12/2010 6:45 PM, Anirban Ghosh wrote:
Thanks a lot for the reply.
But I am getting different results with the two .tpr files (first and
last) using the following commands:
trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 10000 -pbc nojump
trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 10000 -pbc nojump
Did you read trjconv -h about -pbc nojump? Notice how when you didn't
give your command lines last time, you didn't get a very useful answer.
So which .tpr file should I use?
You're trying to measure a membrane thickness. So you want all the
membrane residues in the same box, and don't care about anything else.
There's various ways to use -pbc and -center to achieve this, depending
on what the simulation has done.
Mark
Thanks,
Anirban
On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 4/12/2010 4:33 PM, Anirban Ghosh wrote:
Thanks a lot for the reply.
Actually I am running a protein in lipid bilayer. Now I want to
calculate the thickness of the bilayer at the end of the
simulation.
So for that I want the last structure (.gro) file. So I am
trying to
dump the last structure using trjconv (with -pbc option). So to do
this which .tpr file should I supply to trjconv, the first one
or the
last one?
Since you're not using the coordinates in the .tpr file to extract
the last frame and map its coordinates onto the .tpr's atom names,
it can't matter what they are.
Mark
Thanks again.
Anirban
On 12/4/10, Justin A. Lemkul<jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Anirban Ghosh wrote:
Thanks a lot Justin for the reply. Yes, I understand
that. But ideally
which structure should be used as the reference, in a
general, the
starting structure or the end structure?
That's up to you to decide based on what you need to
measure. Do you want
the
RMSD relative to your starting (i.e. crystal/NMR)
structure, or are you
trying
to study how a protein folds, in which case you'd use the
native (end)
state?
like when I an using trjconv to dump my last frame
(with "-pbc nojump"),
which .tpr file should I use to get the exact picture
of what has
happened to my protein at the end of the simulation.
Should I use the
first .tpr file or the last .tpr file?
I don't understand what you mean. "What has happened" is
an entire
trajectory,
not a snapshot.
-Justin
Thanks a lot again.
Anirban
On Fri, Dec 3, 2010 at 7:35 PM, Justin A.
Lemkul<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Anirban Ghosh wrote:
Hi ALL,
Its a very basic question but still...
When we calculate RMSD (or any other
parameter) using the g_rms
command, we need to supply the .tpr file with
-s option. Now
suppose if I have a total 20 ns simulation
with 4 breaks (i.e 5
ns in each run), then there will be 4 .tpr
files. So at the end
of 20 ns if I wish to calculate RMSD, then
which .tpr file
should I suppy to g_rms, the first one or the
last one? We I run
g_rms with the two .tpr files, I get different
results. So which
one should be used? Any suggestion is welcome.
Use the one that contains the structure you wish
to serve as your
reference.
-Justin
Thanks,
Anirban
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu><http://vt.edu>
| (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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