AMBER Archive (2004)

Subject: Re: AMBER: Comparison of simulation results on amber7 and amber 8

From: Carlos Simmerling (
Date: Wed Oct 06 2004 - 08:36:03 CDT

results from the GB model in AMBER 7 and 8 should match, I've done that
test myself. Make sure that you look at the new variable RGBMAX, it wasn't
in AMBER7 and can affect the comparison. In AMBER7, the RGBMAX was
effectively infinite. Otherwise the results will be completely
comparable, at least
for IGB=1.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:
=================================================================== wrote:

>Dear all amber users,
>I have made some modifications in a protein by attaching different number
>of ligand molecules at selected amino-acid residues. To analyse the effect
>of such changes I will be minimizing the system and then running dynamics
>on it using the GB model.
>I shall be using both amber 7 and 8 to observe the effect of different
>number of ligands on the conformation of the protein.
>1. Will I get substantial differences while comparing the results abtained
>from simulations on amber 7 and amber 8?
>2. Will it be acceptable to compare the results obtained in both the
>situations, if yes then do I need to take care of some specific flags and
>Thanks in adavance for your suggestions,
>With best regards,
>The AMBER Mail Reflector
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