AMBER Archive (2009)

Subject: Re: [AMBER] QM/MM

From: steinbrt_at_rci.rutgers.edu
Date: Tue Jul 28 2009 - 02:19:32 CDT

Hi Bill,

> 1- I am interesting in studying the hydroxyle proton behaviour of one
> compound, So I will use QM/MM WITHOUT shake (i.e. qmshake=0), in this
> case, should I swithoff shake for MM part (i.e. NTC), in other words, is
> it possible to use shake for MM part and no shake for QM/MM part?

I would keep SHAKE on the MM part switched on. It is not uncommon to
remove SHAKE constraints from only a small part of your system and I guess
thats what qmshake is for.

> 2- In case, yes it is possible, should I set detection time (dt) to 0.001
> or 0.002?

I personally would say that removing SHAKE from only a few bonds should
still allow you to run with a delta-t of 0.002. The energy lost/introduced
should be small enough to be compensated by the surroundings or
thermostate. But make sure to check that by comparing runs with dt=0.001
and 0.002. Of course some other constraint in your system may still
require you to use 0.001 for sufficient accuracy...

Regards,

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

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