[gmx-users] Conference "Frontiers in Biomolecular Simulation"
We are proud to announce the 495. Wilhelm und Else Heraeus-Seminar "Frontiers in Biomolecular Simulation" to take place on Jan. 22.-25. 2012 at the Physikzentrum Bad Honnef in Germany. The conference is sponsored by the Heraeus-Foundation, Germany's premier private organisation for the advancement of physics. The conference will deal with the topics of Coarse Grained Models and Methods, Simulating Membranes and Membrane Proteins, Large Scale Quantum Processes and Multiscale and Large Scale Biomolecular Simulation. We are happy to announce that more than 20 distinguished international speakers are committed to make this an intimate, highly productive meeting. Please refer to: http://www.rz.uni-karlsruhe.de/~cd186/ for more information. At the moment, we are encouraging scientists to apply for ca. 30 attendee slots at the meeting which will be filled until Oct. 30th. The conference is free to attend and includes food&lodging, participants only have to cover their own travel costs. We expect slots to fill up very quickly, so please register early. We especially encourage junior group leaders and scientists beginning work in the field of Biomolecular Simulation to attend and present posters on their recent work. Kind Regards, Dr. Thomas Steinbrecher also on behalf of my Co-organizers: Marcus Elstner, Rainer Boeckmann and Christine Peter __ Prof. Dr. Rainer Böckmann Computational Biology Universität Erlangen-Nürnberg Staudtstr. 5 91058 Erlangen Phone:++49 +9131 85-25409 FAX: ++49 +9131 85-25410 E-Mail: rainer.boeckm...@biologie.uni-erlangen.de http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/ ___ -- 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] OPLS and RB parameters in GROMACS
Dear Sulatha, these are probably the more recent parameters from Price, M. L. P., D. Ostrovsky, and W. L. Jorgensen. 2001. Gas-phase and liquid-state properties of 8esters, nitriles, and nitro compounds with the opls-aa force field. J. Comput. Chem. 22:1340– 1352. Best Rainer On Feb 9, 2011, at 6:48 AM, sulatha M. S wrote: > I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, 20, > 4831, 1999), the aliphatic torsional parameters are the same as those from > 1996. here are the values, > > >V1V2 > V3 (kcal/mol) > CT-CT-CT-CT 1.740 -0.157 0.279 > > HC-CT-CT-CT 0.0000.0000.366 > > HC-CT-CT-HC 0.000 0.000 0.318 > > > Values calculated from the equation given in p.62 of the manual in kJ/mol are > > c0 c1 > c2 c3 > CT-CT-CT-CT 3.56686-1.889070.65688 > -2.33467 > > HC-CT-CT-CT 0.66526 1.995770.000 > -2.66102 > > HC-CT-CT-HC 0.76567-2.29702 0.000 > -3.06269 > > and the values given in ffoplsaabon.itp are: > > CT-CT-CT-CT 2.9288-1.46440.2092 > -1.6736 > > HC-CT-CT-CT 0.6276 1.88280 0.000 > -2.5104 > > HC-CT-CT-HC 0.62761.8828 0.000 > -2.5104 > > So there is a difference. Which of these is correct ? Any help is highly > appreciated. > > Sulatha > > > > On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch wrote: > There is no error. The alkane dihedral parameters were updated in 1999, and > differ from those originally published in 1996. > > Andrew > > On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S wrote: > Hi all, > Hi > > I've converted the OPLS-AA torsional potential parameters for the > alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation), > C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the > OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) > to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found > that the calculated values are different. > > A previous post to the gmx-users mailing list on March 27, 2008, > pointed out this issue for the H-C-C-H torsional potential but there was no > response to that. > > Does anyone know if there is an error in the ffoplsaabon.itp file? Or > is there a newer set of OPLS-AA parameters? > > For the OPLS-AA parameters (in kcal/mol), I used: > > dihedral V1 V2 V3 > C-C-C-C1.740 -0.157 0.279 > C-C-C-H 0.0 0.00.366 > H-C-C-H 0.0 0.00.318 > > from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as: > > dihedral C0 C1 C2 C3 > C-C-C-C3.56686 -1.889076 0.65688 -2.33467 > C-C-C-H 0.66526 1.99577 0.0 -2.661024 > H-C-C-H 0.76567 -2.297020.0 -3.06269 > > the parameters in the ffoplsaabon.itp file are: > > dihedral C0 C1 C2 C3 > C-C-C-C 2.9288 -1.4644 0.2092 -1.6736 > C-C-C-H 0.6276 1.882800.0 -2.5104 > H-C-C-H 0.6276 1.8828 0.0 -2.5104 > > > Thankyou for any clarification. > > Sulatha > > -- > 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 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 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/Suppor
Re: [gmx-users] OPLS and RB parameters in GROMACS
Dear Sulatha, these are probably the more recent parameters from Price, M. L. P., D. Ostrovsky, and W. L. Jorgensen. 2001. Gas-phase and liquid-state properties of 8esters, nitriles, and nitro compounds with the opls-aa force field. J. Comput. Chem. 22:1340– 1352. Best Rainer On Feb 9, 2011, at 6:48 AM, sulatha M. S wrote: > I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, 20, > 4831, 1999), the aliphatic torsional parameters are the same as those from > 1996. here are the values, > > >V1V2 > V3 (kcal/mol) > CT-CT-CT-CT 1.740 -0.157 0.279 > > HC-CT-CT-CT 0.0000.0000.366 > > HC-CT-CT-HC 0.000 0.000 0.318 > > > Values calculated from the equation given in p.62 of the manual in kJ/mol are > > c0 c1 > c2 c3 > CT-CT-CT-CT 3.56686-1.889070.65688 > -2.33467 > > HC-CT-CT-CT 0.66526 1.995770.000 > -2.66102 > > HC-CT-CT-HC 0.76567-2.29702 0.000 > -3.06269 > > and the values given in ffoplsaabon.itp are: > > CT-CT-CT-CT 2.9288-1.46440.2092 > -1.6736 > > HC-CT-CT-CT 0.6276 1.88280 0.000 > -2.5104 > > HC-CT-CT-HC 0.62761.8828 0.000 > -2.5104 > > So there is a difference. Which of these is correct ? Any help is highly > appreciated. > > Sulatha > > > > On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch wrote: > There is no error. The alkane dihedral parameters were updated in 1999, and > differ from those originally published in 1996. > > Andrew > > On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S wrote: > Hi all, > Hi > > I've converted the OPLS-AA torsional potential parameters for the > alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation), > C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the > OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) > to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found > that the calculated values are different. > > A previous post to the gmx-users mailing list on March 27, 2008, > pointed out this issue for the H-C-C-H torsional potential but there was no > response to that. > > Does anyone know if there is an error in the ffoplsaabon.itp file? Or > is there a newer set of OPLS-AA parameters? > > For the OPLS-AA parameters (in kcal/mol), I used: > > dihedral V1 V2 V3 > C-C-C-C1.740 -0.157 0.279 > C-C-C-H 0.0 0.00.366 > H-C-C-H 0.0 0.00.318 > > from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as: > > dihedral C0 C1 C2 C3 > C-C-C-C3.56686 -1.889076 0.65688 -2.33467 > C-C-C-H 0.66526 1.99577 0.0 -2.661024 > H-C-C-H 0.76567 -2.297020.0 -3.06269 > > the parameters in the ffoplsaabon.itp file are: > > dihedral C0 C1 C2 C3 > C-C-C-C 2.9288 -1.4644 0.2092 -1.6736 > C-C-C-H 0.6276 1.882800.0 -2.5104 > H-C-C-H 0.6276 1.8828 0.0 -2.5104 > > > Thankyou for any clarification. > > Sulatha > > -- > 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 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 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/Supp
