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> 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>> 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> | (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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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