Tutorial-l Mailing List

From: Seah Harold (bluewolfz_at_hotmail.com)
Date: Wed Feb 20 2008 - 00:56:16 CST

Hi regarding the NAMDS tutorial, i would like to get the appropriate velocity file so that i can get the maxwell boltzmann energy distribution. In the tutorial you gave ubq_wb_eq_1fs.restart.vel in the dir 2-2-maxwell and it specified that rigid bonds are not acceptable and the time step used is 1fs instead of 2fs. So what can i do to get a velocity file that i am able to use for the maxwell boltzmann energy distribution? Can i just delete the line (in bold) rigidBonds or i need to change from all to none?
 
# Integrator Parameterstimestep 2.0 ;# 2fs/steprigidBonds all ;# needed for 2fs stepsnonbondedFreq 1fullElectFrequency 2 stepspercycle 10
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