Hi Atila,
My $0.02 worth. I have also experienced that Gromacs is faster using traditional processors (ie not CUDA). Each program has its advantages and disadvantages. As a beginner I would recommend using Amber because it has some nice tools for building a model and performing the analysis of the trajectory. If you have a nonstandard residue in your model, then getting this incorporated into Gromacs is much more difficult than in Amber. If you are going to extensively modify an existing force field or use your own custom built force field, then this is also easier for a beginner to do in Amber.
Cheers,
Karl
----- Original Message -----
From: "atila petrosian" <atila.petrosian.gmail.com>
To: amber.ambermd.org
Sent: Saturday, December 11, 2010 1:55:49 PM
Subject: [AMBER] comparision of gromacs and amber
Dear amber users
I'm beginner in amber. If I want to do 2 simulations with same condition by
amber and gromacs,
Which of these two programs is faster?
I want to know differences between amber and gromacs.
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Received on Mon Dec 13 2010 - 02:30:03 PST
