[gmx-users] RE : gmx-users Digest, Vol 114, Issue 21
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Wed Oct 9 19:33:16 CEST 2013
OK thank you four kind response. And also thank you and the CHARMM team for this geat job.
On 10/9/13 11:28 AM, ABEL Stephane 175950 wrote:
> Hello Justin,
> Two quick questions, here
> - Since the lipid charmm36 parameters for lipids are already available in the gromacs format on the GROMACS website (charmm36.ff_4.5.4_ref.tgz) from thomas Piggot. Does it means that these files are considered as deprecated and all the users are invited to use in their simulations the CHARMM -GROMACS official release from you ?
AFAIK, the "charmm36.ff_4.5.4_ref.tgz" only contains updated CHARMM36 lipids and
nothing else. Someone please correct me if I am wrong here, but a quick scan
through that archive indicated to me that the force fields for other molecules
(proteins, nucleic acids, etc) were outdated.
Thus, I feel that our new distribution supersedes the available files because
what is contained there is not what we consider the CHARMM36 force field in its
entirety. Users are welcome to use whatever they like, but our distribution is
the only one (to our knowledge) that is equivalent to the current force field
set distributed with CHARMM and does contain an important reparametrization of
the CMAP terms that go along with what we call the CHARMM36 protein force field,
which is probably of particular interest to this community.
> - Did you compare the results for the common molecules, to see if some errors/typos in "charmm36.ff_4.5.4_ref.tgz" were presents ?
We did not look into any errors or typos in other distributions. We created our
files completely on our own directly from existing CHARMM force field files, not
based on anything found in "charmm36.ff_4.5.4_ref.tgz."
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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