AMBER Archive (2006)

Subject: RE: AMBER: AMBER : About the kinetic energy and temperature (GBSA model)

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Mar 28 2006 - 22:35:03 CST

Dear James,

> simulated my system again .The temperature is still very high
> ~ 5123 k . It's
> not reasonable .Why "Sander" didn't correct the
> temperature?Could you give me
> more information about the temperature regulation ,such as
> an example ?

It is very reasonable... The temperature regulation is simply a weak
thermostat, not a rigid constant. If your system's forces are too large it
can easily 'explode' and no amount of temperature regulation will save you.
I can set a bomb off in a freezer and it will still go bang...

A couple of things to try. If you haven't already done so I suggest you work
through the following tutorial.
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/index.htm
this will give you an understanding of how to minimise a system and then
heat it up in controlled fashion. It will also give you an understanding of
shake and timesteps.

Once you have done that go back to your simulation and set ntpr=1 and ntwx=1
and run it for 1000 steps or so nstlim=1000. Then open the resulting mdcrd
file in VMD and it should be immediately obvious what is wrong with your
simulation.

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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