Implicit MD simulations in AMBER

From: Joey Harriman <s808o~at~unb.ca>
Subject: Implicit MD simulations in AMBER
Date: Fri, 24 Oct 2003 11:10:17 -0300

Hi everyone,
 I am currently in the process of running some implicit MD simulations in Amber7.
 As far
 as I can tell the only flags that need to be included in the MD input file are:
 gbsa=1
 igb=1
 extdiel=***
 Can anyone confirm this?  In addition, I am trying to do a MD simulation on a
 ligand in
 Toluene (extdiel=2.4)...are there any suggestions to make this calculation
 faster?  I
 am currently usine SHAKE 2 for the calculations.
 Thanks in advance for your response,
 Joey Harriman
 ----------------------------------
 Joey Harriman
 MSc Computational Chemistry
 University of New Brunswick
 Room 228
 Toole Hall
 s808o~at~unb.ca
 476-6543
 ----------------------------------