[AMBER] Re: about xmin

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 27 Jan 2010 08:36:35 -0500


I've copied this to the amber reflector where you might benefit from
advice wiser and more experienced than just me (especially since I
don't have much experience with QM/MM or using the xmin minimizer.

However, one thing I think you should change is the use of SHAKE, as
this is discouraged (at least in the manual for anything except
minimizations to relieve bad contacts, in which the standard ntmin=1
or 2 would work just fine) for use with minimization (it's primarily a
technique for molecular dynamics). This is controlled by the
variables ntc and ntf for MM, and qmshake for QM.

I can't see anything clearly wrong with the input (except for the
SHAKE issues described above, but I don't think that should cause the
problems you're seeing). I'm guessing more information will help us
diagnose the problem. For instance, does that input file work if you
change ntmin to 1? Do all of the xmin and qm/mm tests pass?
(especially the ones that do a minimization?)

Good luck!

On Wed, Jan 27, 2010 at 3:19 AM, gunajyoti das <guna_das78.yahoo.co.in> wrote:
> Hi Jason,
>    Thank you very much for your suggestion regarding QMMM energy minimization using XMIN. I tried to use the XMIN prcedure by writing the qmmm.in file as follows---
> _______________________________________
>  Initial min of our structure QMMM
>  &cntrl
>   imin=1, maxcyc=1000, ncyc=500,
>   ntmin=3, cut=9.0, ntb=1, ntc=2, ntf=2,
>   ifqnt=1
>  /
>  &qmmm
>   qmmask=':1-6',
>   qmcharge=-4,
>   qmtheory=1,
>   qmshake=1,
>   qm_ewald=1, qm_pme=1
>  /
> ________________________________________
> But the minimization process can not proceed after the first step, and without any error information the process ends. Could you kindly help me out.
> With regards, thanking you.
> Gunajyoti Das
> NEH University
> ________________________________
> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage.

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Wed Jan 27 2010 - 06:00:07 PST
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