[gmx-users] doing restarts

[Justin A. Lemkul]

Juliette N. wrote:
> 
> 
> On 10 September 2011 18:03, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at 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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