Re: [gmx-users] CHARMM36 force field available for GROMACS
Great! Many thanks Justin, and the CHARMM team! Mark On Tue, Oct 8, 2013 at 10:16 PM, 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.htmlhttp://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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] CHARMM36 force field available for GROMACS
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. 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.htmlhttp://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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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 listgmx-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
Re: [gmx-users] CHARMM36 force field available for GROMACS
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.htmlhttp://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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: [gmx-users] CHARMM36 force field available for GROMACS
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.htmlhttp **://mackerell.umaryland.edu/**CHARMM_ff_params.htmlhttp://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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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 listgmx-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
Re: [gmx-users] CHARMM36 force field available for GROMACS
Dear Justin, Thanks for you information. I have a small query on the residue name in the charmm36.ff folder. Is there any document illustrating for the corresponding full name of residues in the .rtp file. As you have illustrated in the file forcefield.doc, the parameters for some carbohydrates such as glucose should be implemented. I found the residues named AALT or AALL should be for glucose, but the names are not easy to understand. Is there any illustration already existing to explain what the abbreviations stand for? Pan 2013/10/9 rajat desikan rajatdesi...@gmail.com 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. 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 -- ==** 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 listgmx-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/Searchbefore 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 listgmx-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 -- Pan Chen CERMAV-CNRS BP 53 38041 Grenoble Cedex 9 tel. +33 (0)4 76 03 76 12 fax. +33 (0)4 76 54 72 03 -- gmx-users mailing listgmx-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
Re: [gmx-users] CHARMM36 force field available for GROMACS
On 10/9/13 7:55 AM, CHEN Pan wrote: Dear Justin, Thanks for you information. I have a small query on the residue name in the charmm36.ff folder. Is there any document illustrating for the corresponding full name of residues in the .rtp file. As you have illustrated in the file forcefield.doc, the parameters for some carbohydrates such as glucose should be implemented. I found the residues named AALT or AALL should be for glucose, but the names are not easy to understand. Is there any illustration already existing to explain what the abbreviations stand for? Residue names come directly from the CHARMM force field files. Since those files are also freely available, you can easily check what is what. The CHARMM files typically include an artistic rendering of the molecule, as best we can do with ASCII :) -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: [gmx-users] CHARMM36 force field available for GROMACS
On 10/9/13 7:54 AM, rajat desikan wrote: 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. I will send you some sample data directly. The outcomes we achieved are equivalent to, or better than, the agreement between CHARMM and GROMACS in the CHARMM27 release that is currently supplied with GROMACS. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: [gmx-users] CHARMM36 force field available for GROMACS
On 10/9/13 7:55 AM, CHEN Pan wrote: Dear Justin, Thanks for you information. I have a small query on the residue name in the charmm36.ff folder. Is there any document illustrating for the corresponding full name of residues in the .rtp file. As you have illustrated in the file forcefield.doc, the parameters for some carbohydrates such as glucose should be implemented. I found the residues named AALT or AALL should be for glucose, but the names are Just to clarify, AALT and AALL are not for glucose, they are alpha-D-altrose and alpha-D-allose, so you can see that the names are as clear and descriptive as we feel we can make them. beta-D-glucose and alpha-D-glucose are BGLC and AGLC, respectively. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: [gmx-users] CHARMM36 force field available for GROMACS
Hi Justin, are you guys planning anything to make pdb2gmx understand the CHARMM patch residues? We have some python scripts which generate new residues based on the patch residues, which allows us to simulate branched molecules (e.g. glycosylation or lignin). But that approach is very suboptimal and I think a more general approach would be very nice. Roland On Tue, Oct 8, 2013 at 4:16 PM, 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. 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-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
Re: [gmx-users] CHARMM36 force field available for GROMACS
On 10/9/13 1:26 PM, Roland Schulz wrote: Hi Justin, are you guys planning anything to make pdb2gmx understand the CHARMM patch residues? We have some python scripts which generate new residues based on the patch residues, which allows us to simulate branched molecules (e.g. glycosylation or lignin). But that approach is very suboptimal and I think a more general approach would be very nice. It's something we're thinking about, though not something we have a generalized solution for at the moment. For example, in CHARMM we generate all nucleic acids as RNA and then patch the 2' site to become DNA. Because of this procedure, we had to hard-code the DNA .rtp entries so that they could be used in GROMACS since there are no DNA entries in the top files. It is just a microcosm of the larger patching architecture that would definitely be useful for polysaccharides and more complex chemical species. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
[gmx-users] CHARMM36 force field available for GROMACS
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. 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
