AMBER Archive (2003)

Subject: AMBER: Implicit MD simulations in Amber7

From: Joey Harriman (s808o_at_unb.ca)
Date: Mon Oct 27 2003 - 12:53:01 CST

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
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