Even with more atoms its entirely reasonable that GB is slower per step.
Check to know for sure.
On Oct 7, 2010 9:40 PM, "patrick wintrode" <pat_wde2.yahoo.com> wrote:
I'm using anber11. I was assuming I should use implicit solvent because to
get a reasonably sized box of explicit solvent, the system will be~45,000
atoms (although forces presumably wouldn't need to be applied to the
solvent). That estimate is based on several standard MD silulations we have
done, plus looking at the space that the most mobile part of the system will
have to travers.
Patrick
--- On Thu, 10/7/10, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Subject: Re: [AMBER] Question about limitations of the nudged elastic band
method
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Thursday, October 7, 2010, 7:49 PM
We really must know what amber version you are using. The neb differs vastly
for a case like yours...
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Received on Thu Oct 07 2010 - 19:00:04 PDT
