Juliette N. wrote:
On 10 September 2011 18:03, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Juliette N. wrote:
Hello,
I am trying to extend a simulation to 2 ns and wanted to know if
I am using the proper tools for this purpose. (version 4.5.4)
1) tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr
-until 2000
mdrun -s old-extend.tpr -cpi old.cpt -o old-extend -c
old-extend -e old-extend
Is what I am doing correct?
Yes. Save yourself some typing with:
mdrun -deffnm old-extend -cpi old.cpt
2) Can I use the following in 4.5.4 instead of above?
mdrun -s old.tpr -cpi old.cpt -append 2000
No. The mdrun -append option does not take an argument; it is a
boolean (i.e. -append/-noappend) to indicate whether old files are
to be appended to or not.
Thank you. Where can I define how long simulation is going to be? I
That's what you're doing with tpbconv -until.
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
think the advantage of append is that it combines old and old-extend
energy files and there is no need for
eneconv -f old-extend.edr old.edr -o concatenate2ns.edr
Is that right?
Correct.
I am just trying to get the most of the tools and skip unnecessary tools
like eneconv as far as it is possible.I am a little confused as there
are different ways explained on "doing restarts" page.
The two 4.x mdrun commands given on that page actually say the same thing. Is
there some way the documentation can be improved? Right now, it's actually
redundant.
tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr -until 2000
mdrun -deffnm old-extend -cpi old.cpt
does this concatenate energy files?
No. That's what -append does. Without -append, you'll get files with .part000X
added to the names and you have to append them later yourself.
-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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