AMBER Archive (2007)

Subject: Re: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Wed Nov 28 2007 - 15:04:32 CST

> Summing up all that I could learn from the literature,I guess that the system
> should be first energy minimized with protein-complex restrain (SHAKE on H
> atoms and PME). For membrane I found indications of ca. 30 kcal/molxA^2. No
> idea how that could be applied to my protein-complex.

I just want to mention that it is generally a bad idea to use SHAKE
for minimizations, since it can lead to unpredictable results.

Gustavo.
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