AW: solvated system for minimization

From: Norman Geist (
Date: Mon Apr 22 2013 - 09:14:20 CDT

Hi Himani,


because the secondary structure of the protein reduces the TOTAL energy and
is supported by hydrogen bonds to water. This TOTAL energy is the main
metric for the minimization. Depending on your initial structure you will
possibly destroy the "good" conformation when running without water and you
will not start your md from a global minimum then. Additionally, the
minimizer will improve the initial positions between the protein and the
water to remove tensions and close contacts, which can blow apart your
molecular system when the md starts.


Norman Geist.


Von: [] Im Auftrag
von Himani Raina
Gesendet: Montag, 22. April 2013 12:31
Betreff: namd-l: solvated system for minimization


Dear namd users


Can anyone tell me why we need to solvate the protein for minimization
config file. Cant we use the protein alone ?


Thanks And Regards 
Himani Raina

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