On 10/9/13 7:03 AM, rajat desikan wrote:
Superb stuff, Justin. Thank you so much. Is it asking too much for a brief
list of the test systems that you used? Thanks again.
We tested everything, at least in terms of representative examples. Single
amino acids, full proteins in vacuo, single nucleotides, full-length ssRNA and
dsDNA, individual lipids with and without water and ions, proteins in solution
with ions, and a wide variety of small molecules interacting with each other.
Everything came out in agreement between the two programs, including everything
that utilized NBFIX terms.
-Justin
On Wed, Oct 9, 2013 at 1:46 AM, Justin Lemkul <jalem...@vt.edu> wrote:
All,
I am pleased to announce the immediate availability of the latest CHARMM36
force field in GROMACS format. You can obtain the archive from our lab's
website at
http://mackerell.umaryland.**edu/CHARMM_ff_params.html<http://mackerell.umaryland.edu/CHARMM_ff_params.html>
.
The present version contains up-to-date parameters for proteins, nucleic
acids, lipids, some carbohydrates, CGenFF version 2b7, and a variety of of
other small molecules. Please refer to forcefield.doc, which contains a
list of citations that describe the parameters, as well as the CHARMM force
field files that were used to generate the distribution.
We have validated the parameters by comparing energies of a wide variety
of molecules within CHARMM and GROMACS and have found excellent agreement
between the two. If anyone has any issues or questions, please feel free
to post them to this list or directly to me at the email address below.
Happy simulating!
-Justin
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==============================**====================
Justin A. Lemkul, Ph.D.
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Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
20 Penn St.
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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