[gmx-users] a question related to tpbconv and trjcat

Acoot Brett acootbrett at yahoo.com
Sat Nov 3 03:00:13 CET 2012

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.



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