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pavan payghan wrote:
I have to recreate .gro file from .trr file by using trjconv which i
have deleated previously for disk space reasons , im using following
commond for that
trjconv -f full.trr -s full.tpr -o fullout.gro .
so my question is will this commond give me the same gro file that it
was previously or it may variate
or any changes that u suggest in the given commond.
No, this will give you the entire trajectory in .gro format, which is likely a
very large file. Use gmxcheck to see for yourself.
my second question is regarding g_rms,
i created the .xvg for g_rms , the grph shows it has continous
run for molecule with some peaks in between why is it so as im doing
analysis for the first time i dont know what does this indicates .
is it because the molecule is jumping across the box ? so that more
rmsd at that place
,i think by using -nojump i can do this ?
That depends on what you define as a peak. Small spikes may or may not be
reasonable, depending on what your structure is doing. If these spikes are very
large, they could correspond to your molecule crossing PBC, in which case you
would have to use trjconv.
-Justin
--
========================================
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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