AMBER Archive (2009)

Subject: Re: [AMBER] RE: question

From: steinbrt_at_rci.rutgers.edu
Date: Thu Nov 05 2009 - 02:12:47 CST

Hi,

> How wrote Marek, we have problem with freeze atoms. I use ibelly for it
> and after simulation, atoms aren't on same place as on the beginning of

IIRC, ibelly appears to be on the way to depreciation and people are
encouraged to use harmonic restraints instead. Even weak restraints will
keep your atoms almost as well fixed as ibelly would, but without
artificially removing degrees of freedom.

> &cntrl
...
> ntt=3,
> gamma_ln=2.0,
...

This is were the problem lies in your run, I believe ntt=3 doesnt check
for ibelly settings and still has virtual particles collide with the
supposedly non-moving atoms. This makes them move a bit, consistent with
your pictures.

Use ntt=1 if you must use ibelly (but be aware that this may introduce
problems as well), or switch to restraints.

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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