[gmx-users] the -extend function of the tpbconv command

[Justin A. Lemkul]

Acoot Brett wrote:
> Dear All,
>  
> I have completed a 1ns production MD. Then I intended to extend it for 
> another 1 ns.
>  
> I use command
>  
> "tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -s next.tpr -cpi previous.cpt"
>  
> I think the results will be automatically attended to previous 
> md_0_1.tpr and md_0_1_noPBC.xtc.
>  

Only if you then run mdrun -append and the files are appended.  tpbconv doesn't 
do any of this for you, it just creates a new run input file capable of running 
a longer simulation.  The fact that you have a file called "md_0_1_noPBC.xtc" 
seems like you've manipulated it in some way, so you shouldn't (and likely 
can't) append to it.  You should append to your original files.

> Then I use "g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns" 
> to get the rmsd.xvg file. Then I use "xmgrace -nxy potential.xvg" to 
> display it. However I find for the  curve the x-axis is from 0 ns to 1 
> ns, not from 0 ns to 2 ns.
>  

If you haven't run a new simulation, you'll only have the data that already exists.

> The definition of "-extend" of the command "tpbconv" is "Extend runtime 
> by this amount (ps)". Thus the commands I used are correct.
>  

You haven't shown us your actual tpbconv command, so there's no way to verify 
that.  In any case, tpbconv doesn't actually extend the simulation, mdrun does.

> Will you please tell me how to process for the extension MD so that the 
> curve of the rmsd.xvg (and all the other xvg files) will have x-axis 
> from the 0 to the 2 ns (2 ns is the total MD time, including the 1 ns 
> extended part)?
>  

There are two steps here:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4

You need to do both.

-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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