[gmx-users] CHARMM36 force field available for GROMACS
jalemkul at vt.edu
Wed Oct 9 13:50:39 CEST 2013
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.
> On Wed, Oct 9, 2013 at 1:46 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 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 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
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
>> (410) 706-7441
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Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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