From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Jul 10 2015 - 02:50:31 CDT
Hi!
That's a very good question!
I've been rolling my own bash/TCL/Python scripts to run simulations in
parts, do equlibration and production runs and to generate templates for
colvars (where you first have to bring the simulation to a certain part of
the colvar-space to do multiple windows, etc...). But lately I've been
wondering exactly the same; am I just reinventing hot water?
So I'd also be interested to know what the best practices for such
workflows are.
All the best,
Ajasja
PS: Here is a link
<http://www.ks.uiuc.edu/Publications/Papers/PDF/GOWE2006/GOWE2006.pdf> to
the paper Tom mentioned.
On 10 July 2015 at 09:38, Thomas C Bishop <bishop_at_latech.edu> wrote:
> This reminds me to ask,
> what are best practices/tools available for NAMD workflows.
>
> There are various qsub & batch management approaches to managing the
> simulation tasks, see e.g. TCBG's Gower2006
> but what _ beginning to end _ solutions are there for the entire process,
> namely:
>
> generating ensembles of systems
> simulating them incl. data management
> analyzing the outputs
> sharing/publishing the data?
>
> Or does this problem not lend itself to a general solution?
>
> TOm
>
> On 07/09/2015 05:53 PM, Ma'Mon Hatmal wrote:
>
> Hi All
>
> I need to call "NAMD" (Molecular Dynamics program) by another program
> (like bat or python script) since it has an input file (config file) and
> output log file?, I need to call it for example 10 times (each time with a
> different input file)...would you please tell me if you have any idea.
>
> Thanks,
>
> *How can we please call "NAMD" from another program? - ResearchGate*.
> Available from:
> https://www.researchgate.net/post/How_can_we_please_call_NAMD_from_another_program
> [accessed Jul 9, 2015].
>
> --
> Dr. Ma'mon Hatmal
> PhD and MSc in Biochemistry and Molecular Biology
> MSc in Global Medicine
> BSc in Medical Laboratory Sciences
>
>
> --
> *******************************
> Thomas C. Bishop
> Associate Professor
> Chemistry & Physics
> Louisiana Tech University
> Tel: 318-257-5209
> Fax: 318-257-3823
> www.latech.edu/~bishop
> ********************************
>
>
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