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

[Justin Lemkul]

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

-- 
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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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