AMBER Archive (2005)

Subject: Re: AMBER: igb10 vlimit exceeded

From: Ray Luo (rluo_at_uci.edu)
Date: Thu Mar 31 2005 - 10:52:50 CST

Wells, David H wrote:

> Web Bug from MailScannerWebBug
>
> I’m trying to simulate a small organic solute in DMSO (83 molecules)
> with igb=10. Previously there was trouble with solvent “penetrating”
> the solute, apparently due to the way the non-bonded list is generated
> in igb=10. That can be gotten around, but now simulations more than 20
> ps are blowing up. The RESTRAINT energy ramps rapidly, vlimits start
> to be breached, and eventually temperature rises rapidly and solvent
> molecules are forcibly ejected from the “cap” (even with FCAP=1000.0).
> Changing igb=10 to igb=0 eliminates the problem.
>
> Are the FCAP restraints only applied on atoms with indexes > NATCAP ?
>
> Any further insights would be appreciated.
>
> Many thanks, Dave
>
Dave,

We have never tested igb=10 with organic solvents, so whatever you see
is all very new to us. I'll be happy to debug it for your simulations.

Best,
Ray 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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