[gmx-users] Re: CHARMM36 force field available for GROMACS

Justin Lemkul jalemkul at vt.edu
Wed Oct 9 17:36:29 CEST 2013

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(proteins, nucleic acids, etc) were outdated.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.
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 | (410) 706-7441


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