AMBER Archive (2009)

Subject: Re: [AMBER] RE: question

From: rrd (rrd_at_seznam.cz)
Date: Thu Nov 05 2009 - 18:09:11 CST

Hi Thomas,

> > &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.

thank you very much for this answer.
You was right and our simulation work correctly now (with sander.MPI as well as with PMEMD).
As wrote Marek, with restrains, there was problem with wt (numbers something about 7000), so for our simplest model, ibelly is very nice way how to do it.
Thank you again.

With kind regards,
    Pavel

> ------------ Původní zpráva ------------
> Od: <steinbrt_at_rci.rutgers.edu>
> Předmět: Re: [AMBER] RE: question
> Datum: 05.11.2009 09:15:09
> ----------------------------------------
> 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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> AMBER_at_ambermd.org
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>
>
>

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