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 apal...@nd.edu 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 mssula...@gmail.com 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/Support/Mailing_Lists __ Prof. Dr.
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 apal...@nd.edu 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 mssula...@gmail.com 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/Support/Mailing_Lists __ Prof. Dr.
Re: [gmx-users] OPLS and RB parameters in GROMACS
Dear Rainer, Thankyou very much. I read the abstract of this paper and it says torsional parameters fro alkanes have been updated. I do not have access to full contents of this paper, so could not get it. Thanks again. Sulatha On Wed, Feb 9, 2011 at 2:27 PM, Rainer Boeckmann rainer.boeckm...@biologie.uni-erlangen.de wrote: 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, V1 V2V3 (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 3.56686-1.88907 0.65688-2.33467 HC-CT-CT-CT 0.66526 1.99577 0.000 -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 apal...@nd.edu 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 mssula...@gmail.com 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
[gmx-users] OPLS and RB parameters in GROMACS
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
Re: [gmx-users] OPLS and RB parameters in GROMACS
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 mssula...@gmail.com 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
Re: [gmx-users] OPLS and RB parameters in GROMACS
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, V1 V2V3 (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 3.56686-1.88907 0.65688-2.33467 HC-CT-CT-CT 0.66526 1.99577 0.000 -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 apal...@nd.edu 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 mssula...@gmail.com 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/Support/Mailing_Lists
Re: [gmx-users] OPLS and RB parameters in GROMACS
On 9/02/2011 4:48 PM, 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, V1 V2V3 (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 I can see nothing relevant on p62 of the 4.5 manual. When giving references to literature that exists in multiple versions, please be very precise. Giving details such as the manual version number, page number, equation number and description of the relationship described in the equation will make it much more likely that someone will (want to) (be able to) help you. Mark c0 c1 c2 c3 CT-CT-CT-CT 3.56686-1.88907 0.65688-2.33467 HC-CT-CT-CT 0.66526 1.99577 0.000 -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 2.9288-1.4644 0.2092 -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 apal...@nd.edu mailto:apal...@nd.edu 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 mssula...@gmail.com mailto:mssula...@gmail.com 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-C 1.740 -0.157 0.279 C-C-C-H 0.0 0.0 0.366 H-C-C-H 0.0 0.0 0.318 from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as: dihedral C0C1 C2C3 C-C-C-C 3.56686-1.8890760.65688 -2.33467 C-C-C-H 0.665261.99577 0.0-2.661024 H-C-C-H 0.76567-2.29702 0.0-3.06269 the parameters in the ffoplsaabon.itp file are: dihedral C0 C1 C2C3 C-C-C-C2.9288 -1.4644 0.2092 -1.6736 C-C-C-H0.62761.88280 0.0-2.5104 H-C-C-H0.62761.8828 0.0-2.5104 Thankyou for any clarification. Sulatha -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto: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
Re: [gmx-users] OPLS and RB parameters in GROMACS
Sorry for not giving the manual version earlier. P. 63 of manual 4.0 is what I am referring to. The equations relate to converting the OPLS torsional parameters to RB parameters in GROMACS with the OPLS ff. The equations are C0 = V0+V2+0.5(V1+V3) C1= 0.5(3 * V3-V1) C2= -V2 + 4 * V4 C3= -2 * V3 C4= -4 * V4 Thanks Sulatha On Wed, Feb 9, 2011 at 11:31 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/02/2011 4:48 PM, 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, V1 V2V3 (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 I can see nothing relevant on p62 of the 4.5 manual. When giving references to literature that exists in multiple versions, please be very precise. Giving details such as the manual version number, page number, equation number and description of the relationship described in the equation will make it much more likely that someone will (want to) (be able to) help you. Mark c0 c1 c2 c3 CT-CT-CT-CT 3.56686-1.88907 0.65688-2.33467 HC-CT-CT-CT 0.66526 1.99577 0.000 -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 apal...@nd.edu 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 mssula...@gmail.comwrote: 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
