AMBER Archive (2002)

Subject: Re: SHAKE troubles

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Wed May 29 2002 - 09:02:15 CDT

Dear Arvid,
this happened to me as well as my system was equilibrated badly. You might
consider slower warming using the &wt option (which helped me) as is
discussed in the DNA tutorial or run short (several ps) MD of the watbox
alone prior to the whole-system MD.

Hope this helps.

Martin
----------------------------------------------------------------------------
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----
Martin Lepsik, PhD student            Phone:  +420/2/20183-540, Fax:
+420/2/20183-292
Dept. of Theor Chem & Center for Complex molecular Systems and Biomolecules
Institute of Organic Chemistry and Biochemistry (IOCB)
Flemingovo nam 2,
Czech Academy of Sciences,
166 10, Prague 6,
Czech Rep.
URL: www.uochb.cas.cz/~teochem

----- Original Message -----
From: "Arvid Soederhaell" <arvid_at_fmp-berlin.de>
To: "amber" <amber_at_heimdal.compchem.ucsf.edu>
Sent: Wednesday, May 29, 2002 12:07 PM
Subject: SHAKE troubles

> Dear all,
> I have some problems with SHAKE that I do not understand. I get the error
> message
>
>      COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
>      DEVIATION IS TOO LARGE
>      NITER, NIT, LL, I AND J ARE :  0 0 1963 3195 3196
>
> no matter what i do???!!! The error message comes from the shake.f
> subprogram. The message implyes that i take a too long timestep, but even
> a timestep of 0.5 fs is too long! (Normally one should be able to use a 2
> fs timestep.) The simulation is stable if i turn off SHAKE and use a
> 0.2 fs timestep. The temperature in the simulation never exceeds 350 K.
>
> Any suggestions to what could be the problem?
>
> (The system is a DPPC lipid membrane with TIP3 water, and I use amber6)
>
> Arvid