[gmx-users] the -extend function of the tpbconv command
Mark.Abraham at anu.edu.au
Wed Apr 4 10:56:12 CEST 2012
On 4/04/2012 6:24 PM, Acoot Brett wrote:
> Hi Justin and All,
> The on-line document on "Extending Simulations" writes,
> "You might want to use the -append option of mdrun
> <http://www.gromacs.org/Documentation/Gromacs_Utilities/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.
Any change is enough to prevent appending. mdrun computed a checksum
when it wrote them, saved the checksums in the checkpoint file, and
demands that newly-computed ones match when attempting to append later.
Use only the original trajectory files when attempting to append.
> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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