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?
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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