Re: [gmx-users] Minimization stops without reaching the requested precision Fmax < 1000
Already replied https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-June/125707.html Which just links to http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision which explains what the error message means. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 25 Jun 2019 at 19:51, Mahdi Bagherpoor wrote: > > Dear Gromacs Users, > > I am trying to add the tetrahedral zinc atom dummy model into CHARMM36 > force field in Gromacs. In my system, this dummy zinc interact with four > Cystein residues (CYM). The parameters of the zinc are available in CHARMM > format, which I used to use it in NAMD package. After adding appropriate > parameters, when I do energy minimization, I get this error: > > > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 1000 (which may not be possible for your system). > ... > Steepest Descents converged to machine precision in 1045 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -1.5922652e+06 > Maximum force = 3.2106902e+07 on atom 3526 > Norm of force = 1.4857810e+05 > > > Atom 3526 is dummy atom of zinc ion. The dummy parameters added in > ffbonded.itp file are: > -- ffbonded.itp > > ;zinc dummy model, bonds > HK ZD 1 0.0900451872.00 > HK HK 1 0.1470451872.00 > ;zinc dummy model, angles > HK ZD HK 5 109.50 460.24 0. > 0.00 > HK HK HK 560.00 460.24 0. > 0.00 > HK HK ZD 535.25 460.24 0. > 0.00 > ;zinc dummy model, dihedrals > ZD HK HK HK 935.30 0.00 2 > HK ZD HK HK 9 120.00 0.00 2 > HK HK HK HK 970.00 0.00 2 > > --- ffnonbonded.itp > > ;zinc dummy model >ZD3061.380.000 A 0.3100 0.1 >HK 1 1.0080000.500 A 0. 0.0 > > = > In contrast to Gromacs, when I do minimization in NAMD, there is no such an > error in minimization. I should mention that I am using single precision > platform of Gromacs. > I would appreciate if you could share me in case you have some ideas about > this problem. > > Cheers, > Mahdi > -- > 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. -- 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.
[gmx-users] Minimization stops without reaching the requested precision Fmax < 1000
Dear Gromacs Users, I am trying to add the tetrahedral zinc atom dummy model into CHARMM36 force field in Gromacs. In my system, this dummy zinc interact with four Cystein residues (CYM). The parameters of the zinc are available in CHARMM format, which I used to use it in NAMD package. After adding appropriate parameters, when I do energy minimization, I get this error: Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). ... Steepest Descents converged to machine precision in 1045 steps, but did not reach the requested Fmax < 1000. Potential Energy = -1.5922652e+06 Maximum force = 3.2106902e+07 on atom 3526 Norm of force = 1.4857810e+05 Atom 3526 is dummy atom of zinc ion. The dummy parameters added in ffbonded.itp file are: -- ffbonded.itp ;zinc dummy model, bonds HK ZD 1 0.0900451872.00 HK HK 1 0.1470451872.00 ;zinc dummy model, angles HK ZD HK 5 109.50 460.24 0. 0.00 HK HK HK 560.00 460.24 0. 0.00 HK HK ZD 535.25 460.24 0. 0.00 ;zinc dummy model, dihedrals ZD HK HK HK 935.30 0.00 2 HK ZD HK HK 9 120.00 0.00 2 HK HK HK HK 970.00 0.00 2 --- ffnonbonded.itp ;zinc dummy model ZD3061.380.000 A 0.3100 0.1 HK 1 1.0080000.500 A 0. 0.0 = In contrast to Gromacs, when I do minimization in NAMD, there is no such an error in minimization. I should mention that I am using single precision platform of Gromacs. I would appreciate if you could share me in case you have some ideas about this problem. Cheers, Mahdi -- 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.
Re: [gmx-users] Minimization stops without reaching the requested precision Fmax < 1000
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 25 Jun 2019 at 04:03, Mahdi Bagherpoor wrote: > > Dear Gromacs Users, > > I am trying to add the tethrahedral zinc atom dummy model into CHARMM36 > force field in Gromacs. In my system, this dummy zinc interact with four > Cystein residues (CYM). The parameters of the zinc are available in CHARMM > format, which I used to use it in NAMD package. After adding appropriate > parameters, when I do energy minimization, I get this error: > > > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 1000 (which may not be possible for your system). > ... > Steepest Descents converged to machine precision in 1045 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -1.5922652e+06 > Maximum force = 3.2106902e+07 on atom 3526 > Norm of force = 1.4857810e+05 > > > Atom 3526 is dummy atom of zinc ion. The dummy parameters added in > ffbonded.itp file are: > -- ffbonded.itp > > ;zinc dummy model, bonds > HK ZD 1 0.0900451872.00 > HK HK 1 0.1470451872.00 > ;zinc dummy model, angles > HK ZD HK 5 109.50 460.24 0. > 0.00 > HK HK HK 560.00 460.24 0. > 0.00 > HK HK ZD 535.25 460.24 0. > 0.00 > ;zinc dummy model, dihedrals > ZD HK HK HK 935.30 0.00 2 > HK ZD HK HK 9 120.00 0.00 2 > HK HK HK HK 970.00 0.00 2 > > --- ffnonbonded.itp > > ;zinc dummy model >ZD3061.380.000 A 0.3100 0.1 >HK 1 1.0080000.500 A 0. 0.0 > > = > In contrast to Gromacs, when I do minimization in NAMD, there is no such an > error in minimization. I should mention that I am using single precision > platform of Gromacs. > I would appreciate if you could share me in case you have some ideas about > this problem. > > Cheers, > Mahdi > -- > 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. -- 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.
[gmx-users] Minimization stops without reaching the requested precision Fmax < 1000
Dear Gromacs Users, I am trying to add the tethrahedral zinc atom dummy model into CHARMM36 force field in Gromacs. In my system, this dummy zinc interact with four Cystein residues (CYM). The parameters of the zinc are available in CHARMM format, which I used to use it in NAMD package. After adding appropriate parameters, when I do energy minimization, I get this error: Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). ... Steepest Descents converged to machine precision in 1045 steps, but did not reach the requested Fmax < 1000. Potential Energy = -1.5922652e+06 Maximum force = 3.2106902e+07 on atom 3526 Norm of force = 1.4857810e+05 Atom 3526 is dummy atom of zinc ion. The dummy parameters added in ffbonded.itp file are: -- ffbonded.itp ;zinc dummy model, bonds HK ZD 1 0.0900451872.00 HK HK 1 0.1470451872.00 ;zinc dummy model, angles HK ZD HK 5 109.50 460.24 0. 0.00 HK HK HK 560.00 460.24 0. 0.00 HK HK ZD 535.25 460.24 0. 0.00 ;zinc dummy model, dihedrals ZD HK HK HK 935.30 0.00 2 HK ZD HK HK 9 120.00 0.00 2 HK HK HK HK 970.00 0.00 2 --- ffnonbonded.itp ;zinc dummy model ZD3061.380.000 A 0.3100 0.1 HK 1 1.0080000.500 A 0. 0.0 = In contrast to Gromacs, when I do minimization in NAMD, there is no such an error in minimization. I should mention that I am using single precision platform of Gromacs. I would appreciate if you could share me in case you have some ideas about this problem. Cheers, Mahdi -- 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.
