AMBER Archive (2007)

Subject: Re: AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Nov 06 2007 - 05:49:13 CST

you will have no problems combining MD data from Amber 8 and 9.
they work essentially the same way.

On Nov 6, 2007 3:30 AM, ming hui <yongminghui_at_gmail.com> wrote:

> Dear Amber users,
>
> I have been using AMBER 8 to run standard MD simulations a protein and its
> mutants for my project, however now due to restraints of my current computer
> cluster, I have to use another cluster that only has AMBER 9 to simulate
> some of the mutants.
> If I use the same forcefield (or parameterize everything first in amber 8)
> and my input parameters (ntf,ntt etc) are the same as those taken in AMBER
> 9, is there any significant difference in the way AMBER 9 works that would
> make it unfair for me to compare the simulations that were run on different
> versions? I know the thermodynamic integration method has changed, but I'm
> not as sure about normal simulations.
>
> Thank you
>
> Regards,
> Ming Hui
>

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