Re: log file from 3 different protein simulations

From: Axel Kohlmeyer (
Date: Mon Feb 16 2009 - 09:13:31 CST

On Mon, 16 Feb 2009, sripad chandan wrote:

SP> Dear friends,
SP> I have log file of md simulation of 3 different proteins (A, B, C).
SP> I want to plot energy in a single plot.
SP> I tried with cat command and looks its not working.

please note that "is not working" is not a very helpful description.
you have to say what you did, what you expected to get, and what
you got instead. otherwise a person would need psychic powers to
determine what went wrong.

SP> can anyone help me in this regard?

you should think about what cat does before blindly using it.
and you should think about what logfile analysis tools do.
of course, in your case you have to produce 3 different data
sets and then use a regular graphing tool to produce a combined
plot. unless you program it yourself, there will almost never
be a "just click here" tool that does exactly what you want.

SP> and is there any resource to find analysis tools (list, name) for molecular
SP> dynamics simulation result analysis (like Electrostatic interaction energy
SP> maps, correlation matrix etc)?

you forgot to ask: is there a script that writes my thesis?


SP> thanks in advance.
SP> chandan

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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