Thanks for your input, Justin. Helpful as always.
I am assuming the array is formatted to vary phi as a function of psi i.e. (-180,-180), (-180,-165), (-180,-150) [considering (phi,psi)] and again but for phi = -165. I am also assuming that, since it is a 24x24 matrix, values will start in phi=-180,psi=-180 but will end in phi=165, psi=165. Only a 25x25 matrix would lead to end in phi=180,psi=180, but since they -180 and 180 are equivalent, maybe GROMACS already do this workaround? The last question: are those values in kJ/mol? Cheers! -- Marcelo > The \ are line continuation characters, so GROMACS is reading a 24x24 > matrix in a single array of values. > > The values are written for all values of phi at a given value of psi, > i.e. writing each row of the matrix, starting from phi = -180, psi = > -180 until phi = 180, psi = 180. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 4 > Date: Tue, 7 Jan 2020 11:40:30 +0900 > From: ??? <byunjy0...@gmail.com> > To: gmx-us...@gromacs.org > Subject: [gmx-users] The maxwarn fatal errors > Message-ID: <4b64c77f-360f-44ca-b051-11df14d7f...@gmail.com> > Content-Type: text/plain; charset=us-ascii > > Dear everyone, Happy New year! > I have gone through the Justin Lemku tutorial for Umbrella Sampling. > During tutorial, When I treid to input the command line: > gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r > npt0.gro -n index.ndx -o umbrella0.tpr > > I have met two warnings and they occured fatal error.: > Fatal error: > Too many warnings (2). > If you are sure all warnings are harmless, use the -maxwarn option. > > And the waring is: > WARNING 1 [file topol.top, line 56]: > The GROMOS force fields have been parametrized with a physically > incorrect multiple-time-stepping scheme for a twin-range cut-off. When > used with a single-range cut-off (or a correct Trotter > multiple-time-stepping scheme), physical properties, such as the density, > might differ from the intended values. Since there are researchers > actively working on validating GROMOS with modern integrators we have not > yet removed the GROMOS force fields, but you should be aware of these > issues and check if molecules in your system are affected before > proceeding. Further information is available at > https://redmine.gromacs.org/issues/2884 , and a longer explanation of > our > decision to remove physically incorrect algorithms can be found at > https://doi.org/10.26434/chemrxiv.11474583.v1 . > > > WARNING 2 [file md_umbrella.mdp]: > With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p (1) > should be at least twice as large as tau-t (1) to avoid resonances > > I solved this problem with using -maxwarn option but I am wondering > whether thses warning is passed over. > What do you think what I happend? dears. Any idea on what caused this > problem? > > ------------------------------ > > Message: 5 > Date: Mon, 6 Jan 2020 21:41:28 -0500 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] The maxwarn fatal errors > Message-ID: <89785204-b49e-4f0c-3da9-10abd0b13...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 1/6/20 9:40 PM, ??? wrote: > > Dear everyone, Happy New year! > > I have gone through the Justin Lemku tutorial for Umbrella Sampling. > During tutorial, When I treid to input the command line: > > gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r > npt0.gro -n index.ndx -o umbrella0.tpr > > > > I have met two warnings and they occured fatal error.: > > Fatal error: > > Too many warnings (2). > > If you are sure all warnings are harmless, use the -maxwarn option. > > > > And the waring is: > > WARNING 1 [file topol.top, line 56]: > > The GROMOS force fields have been parametrized with a physically > > incorrect multiple-time-stepping scheme for a twin-range cut-off. When > > used with a single-range cut-off (or a correct Trotter > > multiple-time-stepping scheme), physical properties, such as the > density, > > might differ from the intended values. Since there are researchers > > actively working on validating GROMOS with modern integrators we have > not > > yet removed the GROMOS force fields, but you should be aware of these > > issues and check if molecules in your system are affected before > > proceeding. Further information is available at > > https://redmine.gromacs.org/issues/2884 , and a longer explanation > of our > > decision to remove physically incorrect algorithms can be found at > > https://doi.org/10.26434/chemrxiv.11474583.v1 . > > > > > > WARNING 2 [file md_umbrella.mdp]: > > With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p > (1) > > should be at least twice as large as tau-t (1) to avoid resonances > > > > I solved this problem with using -maxwarn option but I am wondering > whether thses warning is passed over. > > What do you think what I happend? dears. Any idea on what caused this > problem? > > The first warning is very verbose and provides you with substantial > justification and background reading. > > As for the second, change tau-p to 2 as suggested. Note that I have not > made any attempt to update the tutorials for the 2020 version, and they > are only guaranteed to be compatible with GROMACS 2018.x versions. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 189, Issue 13 > ****************************************************** > -- -- Marcelo Depólo Polêto Postdoctoral Researcher BIOAGRO - Room T07 Department of General Biology - UFV Contact: + 55 31 3612-2464 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.