Thank you, Justin. I am particularly interested in the lipid simulations. Can you upload the final results on dropbox? Sorry for the trouble...I intend to simulate a membrane-protein system using charmm36. I will let you know how that goes. Thanks.
On Wed, Oct 9, 2013 at 5:20 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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<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 >>> >>> -- >>> ==============================****==================== >>> >>> >>> 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@outerbanks.umaryland.****edu <jalemkul@outerbanks.** >>> umaryland.edu <jalem...@outerbanks.umaryland.edu>> | >>> (410) 706-7441 >>> >>> ==============================****==================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> >>> * Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >> >> >> > -- > ==============================**==================== > > 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@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
