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. Amber11 allows explicit solvent. Your system is
likely to be very inefficient in GB, not to me.tion accuracy issues. Amber11
neb should be reasonable. Of course you will need careful validation.
On Oct 7, 2010 8:43 PM, "patrick wintrode" <pat_wde2.yahoo.com> wrote:
Hi all,
I'm studying a conformational change in a large protein. Using implicit
solvent, the system size is ~5,000 atoms (45 kD protein). Crystal structures
are available for both the start and end states. The conformational change
is quite large: one part of the protein moves nearly 40 angstroms, and most
of the structure moves somewhat in response, so it's not clear that forces
can be applied to only part of the system.
I'm working through the NEB tutorial now, but before I invest too much time,
I want to check that I'm not wildly overestimating the size of the systems
that the NEB method can realistically handle. I have access to a reasonably
large computing cluster with ~1,200 processors.
Based on the above, does this sound like a feasible application of NEB?
Thanks.
Patrick L. Wintrode
Department of Physiology & Biophysics
Case Western Reserve University
Cleveland, Ohio, 44106
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Received on Thu Oct 07 2010 - 19:00:03 PDT
