AMBER Archive (2008)

Subject: AMBER: Free energy landscape? HOWTO?

From: Yi-Ming Cheng (d90223013_at_ntu.edu.tw)
Date: Mon Mar 31 2008 - 03:12:05 CDT

Hello,
I came across a problem about generating a free energy landscape. The
details are presented as follows. I¡¦ve done a simulation of a peptide
(31mer with ~2000 explicit water) by using replica exchange molecular
dynamics simulation (REMD) method with AMBER ff03 force field. A total
of 32 replicas are employed, covering the temperature range from 280
to 465 K. Individual simulation lengths of 10 ns sum up to a total
simulation time of 0.32 microsecond. It was shown in the REMD results
that the helical contents toward the N- and C-terminus regions as well
as the helix of gyration for whole peptide varied significantly during
the folding simulation. Also, the time series of the root-mean
square-deviation of the backbone atoms shows that the peptide tends to
converge in a specific way. So I am trying to strengthen the converged
result by using a free energy landscape.
Ps. I¡¦ve read some of the Wolynes¡¦ papers already. The problem is that
I still don¡¦t know how to do it after I read those papers. So it would
be a huge favor to me and would be largely appreciated if someone can
give me a simple demonstration about how to do with the free energy
landscape.

Yi-Ming Cheng

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