On 11/2/12 10:00 PM, Acoot Brett wrote:
Dear All
First I ran a 5 ns MD (md-0ns-5ns), I get md-0ns-5ns.tpr and
md-0ns-5ns.cpt,then I extend it for 1 ns by
tpbconv -s tpbconv -s md-0ns-5ns.tpr -extend 1000 -o md-5ns-to-6ns.tpr
mdrun -deffnm md-5ns-to-6ns -cpi md-0ns-5n.cpt
Then I further extend it for 2 ns by
tpbconv -s md-5ns-to-6ns.tpr -extend 2000 -o md-6ns-to-8ns.tpr
mdrun -deffnm md-6ns-to-8ns -cpi md-5ns-to-6ns.cpt
Then I connect all the above 3 MDs together. First I connect the first 2:
trjcat -f md-0ns-5ns.trr md-5ns-to-6ns.trr -o md-0ns-6ns.trr
Then I connect the output md-0ns-6ns.trr with md-6ns-to-8ns.trr by
trjcat -f md-0ns-6ns.trr md-6ns-to-8ns.trr -o md-0ns-8ns.trr
Now I want to extract the PDB files at different time intervals from
md-0ns-8ns.trr.
If I extract the PDB from md-0ns-8ns.trr at 1 ns, I can use the following
command I think:
trjconv -f md-0ns-8ns.trr -s md-0ns-5ns.tpr -o md-0ns-8ns_extracted_at_1ns.pdb
-dump 1000.
Here is my question. If I want to extract the PDB from md-0ns-8ns.trr at 7 ns,
should I use the command
trjconv -f md-0ns-8ns.trr -s md-0ns-5ns.tpr -o md-0ns-8ns_extracted_at_7ns.pdb
-dump 7000,
or should I use the following command
trjconv -f md-0ns-8ns.trr -s md-5ns-to-6ns.tpr -o
md-0ns-8ns_extracted_at_7ns.pdb -dump 7000
I am looking forward to getting your reply.
In this case, the choice of .tpr file is irrelevant; trjconv only uses the .tpr
to write atom and residue names and numbers. In reality, the different .tpr
files contain identical information with the exception of the number of steps
specified in each.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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