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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