Re: [AMBER] SHAKE flucatuation

From: Thomas Cheatham <>
Date: Thu, 10 Oct 2013 14:37:40 -0600 (Mountain Daylight Time)

> I think this is your problem. Set ioutfm=1 to print a NetCDF file instead
> of ASCII trajectory file. In your simulation, I believe that the bonds ARE
> being constrained to the same values (the SETTLE algorithm is analytical),
> but your trajectory is printed out in a precision with only 3 decimal
> places! Using NetCDF trajectories will store numbers to higher precision
> and give you a more accurate measure of bond lengths.

Yes, Jason is correct as usual. My previous e-mail was measuring ascii
trajectory error. With NetCDF, std dev of bond length is ~2x10**-6 A and
0.0002 degrees for the angle... --tec3

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Received on Thu Oct 10 2013 - 14:00:05 PDT
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