Hi Sundar,
general advice: check the literature on what other people did to get
insight into similar problems. This should give you a good overview what
can be done by MD - and what can't. Interaction and fluctuation can be
assessed via energy analysis (g_energy, one energygroup per amino acid),
and distance plots (g_dist). Fluctuations are distinguishable via the
RMSF analysis (g_rmsf). And: check the manual + the GROMACS wiki again.
greetings
Steffen
hi people,
I am new to gromacs. I am running gromacs (version 3.3.1) for a
protein and its 3 mutants. I am not having any problems in the
run. I would like to focus my analysis on 3-4 amino acids
specifically.
Can anyone please tell me some good commands or a link where I can check
how these amino acids are interacting, how these amino acids are
fluctuating etc.
I searched the manual but I am not sure which commands to use.
Also, I think it is better to get some help from people who have done this
type of analysis many times.
I am waiting for your reply.
Thank you
--
Dipl.-Chem. Steffen Wolf
Fellow of the Ruhr-University Research School
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: [EMAIL PROTECTED]
Web: http://www.bph.rub.de
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