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

Acoot Brett acootbrett at yahoo.com
Wed Apr 4 10:24:23 CEST 2012

Hi Justin and All,
The on-line document on "Extending Simulations" writes,
"You might want to use the -append option of mdrun to append the new output to the old files. Note that this will only work when the old output files have not been modified by the user.  Appending is the default behavior as of version 4.5."
We can see "Appending is the default behavior as of version 4.5", and what I use is version 4.5. Thus for mdrun, even without mention "-append " appending should be automatically done.
In addition, after the old output files were created, I only use the "trjconv" to process them, and I did not modify them.
Thus the reason why the extended part output files were not automatically appended to my original old outputfiles according to what I have done (tpbconv -s previous.tpr -extend timetoextendby -o next.tpr       mdrun -s next.tpr -cpi previous.cpt) is still unclear.
Will you please give an explaination?

 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, 4 April 2012 10:36 AM
Subject: Re: [gmx-users] the -extend function of the tpbconv command

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:


You need to do both.


-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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