From: Aditya Ranganathan (aditya.sia_at_gmail.com)
Date: Fri Mar 05 2010 - 21:59:26 CST
Hi Everyone,
I`m trying to simulate a system of 2 ACTH and 2 Beta Endorphin peptides and
intend to study the interaction between them. I first minimized the peptides
before solvating it (and added Na and Cl ions to neutralize the box) and
then minimized the solvated system again. I then heated the system slowly
for 300ps with an increment of 0.001K per step and then equilibrated the
system at 300K for another 300ps.
I then started the final production run and intend to run it for a minimum
of 10 ns to study any interaction or aggregation tendency between the
peptides. However, what started as a Cubical waterbox initially has now
become an almost cylindrical shaped water `box`. The configuration I`ve used
is of an NVT simulation. However, even in the cylindrical system, the
peptides are fully surrounded by water and not exposed out of the solvent.
The simulation has now run for almost 4ns and still continues to run without
any crashes or errors.
However my question is whether the change in shape of the water box is a
sign of an inappropriate simulation or an undesirable change.
Thanks,
Srivastav Ranganathan (Aditya)
Junior Research Assistant
Department of Biosciences and Bioengineering,
IIT Bombay,
Mumbai-400076
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