Re: [AMBER] Equilibration

From: Bill Ross <>
Date: Wed, 22 Nov 2017 01:51:30 -0800

A phase change might be of interest in its own right. You might want to
try rms fitting different regions from coords right before and right
after, to figure out what changed, and whether it means anything
Nobel-related or about the quality of your equilibration. If nothing
else, it will sharpen your sleuthing ability.

Ir maybe someone with actual protein experience can comment on it.
Ideally you should be able to search people's equilibration graphs for


On 11/21/17 11:03 PM, wrote:
> Dear Bill,
> In solvating the protein 27523 water molecules were used. Moreover, to
> balance charges 199 Na+ and 199 Cl- ions were used. I do not see any
> considerable change in the movie.
> Best Regards,
> Sara.
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Nov 22 2017 - 02:00:02 PST
Custom Search