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.
Mark
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?
Cheers,
Acoot
*From:* Justin A. Lemkul <[email protected]>
*To:* Acoot Brett <[email protected]>; Discussion list for GROMACS
users <[email protected]>
*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:
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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