AMBER Archive (2006)

Subject: AMBER: restraints and constant pressure

From: Joshua (jb1978j_at_excite.com)
Date: Fri Sep 15 2006 - 00:44:09 CDT

AMBER users,

I was hoping that somebody could clarify something that I found in an AMBER tutorial. In this tutorial:

http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/section5.htm

it says:

"Using constant pressure with restraints can also cause problems so initially we will run 20 ps of MD at constant volume."

I am working with a system where it is really necessary to use restraints on about one third of the solute. I had planned on using ntr=1 with a force constant of 10 kcal/mol. Could someone please specify what the risks are of combining restraints with constant pressure, and how I can minimize those risks?

Thank you very much for your help.

Josh

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