RE: [gmx-users] How to increase the number of parameters in dihedral angle potentials?
Hi, I already answered this mail, but somehow for a small fraction of the mails I reply to hotmail replies to the user, not to the list. Here is my answer: You can't do this easily. The current maximum for the number of parameters per interaction is 6. If you really want to, you could increase this, as well as NR_RBDIHS in include/types/idef.h. This would make your tpr files incompatible with the standard release binaries. Another option would be to use tabulated dihedral functions, then you can do anything you want (see the manual). Berk > Date: Tue, 23 Jun 2009 10:16:45 +1000 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] How to increase the number of parameters in dihedral > angle potentials? > > bh...@princeton.edu wrote: > > Dear all, > > > > This is the problem I meet with. GROMACS provides a Ryckaert-Bellemans > > function with 6 parameters (C0, C1, C2, ..., C5) , while what I need is a > > function of summation over 8 terms, that is, 8 parameters from C0 to C7. I > > tried to add the values of the two additional pamameters at the end of > > each lines in the section of dihedral angles in the 'molecule.itp' file. > > The 'grompp' command then gave an error information, saying there could > > only be either 6 or 12 parameters for Ryckaert-Bellemans potentials. > > If you read the description of R-B in the manual, it only allows for > 6-parameter R-B. It's not obvious (see footnote to table 5.4, at least), > but the other are for free energy calculations that might be varying > these parameters. > > >So I added 4 zeros for the rest 4 parameters in 'molecule.itp'. Now, the > >'grompp' command did not gave error information any more and I run the > >simulation with a 12-parameter Ryckaert-Bellemans potential. The problem is > >that the trajectory obtained from 12-parameter RB potential is exactly the > >same as the trajectory having generated by 6-parameter RB potential. That > >means the newly added 6 parameter values can not be recognized by GROMACS. > >Has anyone met with such kind of problems? > > Hence, your observations. Since you're not running FE, the 7th and 8th > are never being used for anything. > > >What did you do to make GROMACS recognize 6 more parameters in RB > >potentials? > > You can't. You would have to either implement your own bonded function, > or use a table lookup for this bonded interaction. See manual section 4.2.13 > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to increase the number of parameters in dihedral angle potentials?
bh...@princeton.edu wrote: Dear all, This is the problem I meet with. GROMACS provides a Ryckaert-Bellemans function with 6 parameters (C0, C1, C2, ..., C5) , while what I need is a function of summation over 8 terms, that is, 8 parameters from C0 to C7. I tried to add the values of the two additional pamameters at the end of each lines in the section of dihedral angles in the 'molecule.itp' file. The 'grompp' command then gave an error information, saying there could only be either 6 or 12 parameters for Ryckaert-Bellemans potentials. If you read the description of R-B in the manual, it only allows for 6-parameter R-B. It's not obvious (see footnote to table 5.4, at least), but the other are for free energy calculations that might be varying these parameters. So I added 4 zeros for the rest 4 parameters in 'molecule.itp'. Now, the 'grompp' command did not gave error information any more and I run the simulation with a 12-parameter Ryckaert-Bellemans potential. The problem is that the trajectory obtained from 12-parameter RB potential is exactly the same as the trajectory having generated by 6-parameter RB potential. That means the newly added 6 parameter values can not be recognized by GROMACS. Has anyone met with such kind of problems? Hence, your observations. Since you're not running FE, the 7th and 8th are never being used for anything. What did you do to make GROMACS recognize 6 more parameters in RB potentials? You can't. You would have to either implement your own bonded function, or use a table lookup for this bonded interaction. See manual section 4.2.13 Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] How to increase the number of parameters in dihedral angle potentials?
Dear all, This is the problem I meet with. GROMACS provides a Ryckaert-Bellemans function with 6 parameters (C0, C1, C2, ..., C5) , while what I need is a function of summation over 8 terms, that is, 8 parameters from C0 to C7. I tried to add the values of the two additional pamameters at the end of each lines in the section of dihedral angles in the 'molecule.itp' file. The 'grompp' command then gave an error information, saying there could only be either 6 or 12 parameters for Ryckaert-Bellemans potentials. So I added 4 zeros for the rest 4 parameters in 'molecule.itp'. Now, the 'grompp' command did not gave error information any more and I run the simulation with a 12-parameter Ryckaert-Bellemans potential. The problem is that the trajectory obtained from 12-parameter RB potential is exactly the same as the trajectory having generated by 6-parameter RB potential. That means the newly added 6 parameter values can not be recognized by GROMACS. Has anyone met with such kind of problems? What did you do to make GROMACS recognize 6 more parameters in RB potentials? Thanks Bingster ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
