Re: [gmx-users] Re: single point calculation with gromacs
On Wed, Nov 6, 2013 at 4:07 PM, fantasticqhl fantastic...@gmail.com wrote: Dear Justin, I am sorry for the late reply. I still can't figure it out. It isn't rocket science - your two .mdp files describe totally different model physics. To compare things, change as few things as necessary to generate the comparison. So use the same input .mdp file for the MD vs EM single-point comparison, just changing the integrator line, and maybe unconstrained-start (I forget the details). And be aware of http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy Mark Could you please send me the mdp file which was used for your single point calculations. I want to do some comparison and then solve the problem. Thanks very much! All the best, Qinghua -- View this message in context: http://gromacs.5086.x6.nabble.com/single-point-calculation-with-gromacs-tp5012084p5012295.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: single point calculation with gromacs
Dear Justin, I am sorry for the late reply. I still can't figure it out. Could you please send me the mdp file which was used for your single point calculations. I want to do some comparison and then solve the problem. Thanks very much! All the best, Qinghua -- View this message in context: http://gromacs.5086.x6.nabble.com/single-point-calculation-with-gromacs-tp5012084p5012295.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: single point calculation with gromacs
Dear Justin, *Thanks very much for your reply! Here is my minim.mdp I used:* /; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 0 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) rlist = 9.0 ; Cut-off for making neighbor list (short range forces) coulombtype = Cut-off ; Treatment of long range electrostatic interactions rcoulomb= 9.0 ; Short-range electrostatic cut-off rvdw= 9.0 ; Short-range Van der Waals cut-off pbc = no; Periodic Boundary Conditions (yes/no) / *If I used this mdp file for 0-step minimization, I could get potential energy around 700 kJ/mol for my system. But I would get potential energy around 2.6e+05 kJ/mol if I used the mdv.mdp (md simulation in vacuum) for calculations with rerun option. And the bond potential could also reach as high as 1.1e+05 kJ/mol. Actually, my system is very small, it contains only 37 atoms. I believe that the energy reported by 0-step minimization were more reasonable. So I guess that there might be some problem for the mdp file usd with rerun, and here is the mdv.mdp:* /define = ;-DPOSRES integrator = md ; molecular dynamics algorithm tinit = 0.0 ; start time and timestep in ps dt = 0.002; time step in ps nsteps = 2; number of steps for 1000ns run emtol = 100; convergence criterion emstep = 0.05 ; intial step size nstlist = 0 ; step frequency for updating neighbour list ns_type = simple ; method for neighbour searching (?) nstxout = 1; frequency for writing coords to output .trr file nstvout = 1 ; frequency for writing velocities to output...should be same as nstxout nstfout = 1; frequency for writing forces to output nstlog = 1 ; frequency for writing energies to log file nstenergy = 1 ; frequency for writing energies to energy file nstxtcout = 1 ; frequency for writing coords to xtc traj xtc_grps= system ; group(s) whose coords are to be written in xtc traj energygrps = system ; group(s) whose energy is to be written in energy file pbc = no ; use pbc rlist = 0 ; cutoff lengths (nm) epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range or DC of reaction field niter = 100 ; Some thingies for future use fourierspacing = 0.16 fourier_nx = 30 fourier_ny = 30 fourier_nz = 30 coulombtype = Cut-off ; truncation for minimisation, with large cutoff rcoulomb= 0 rcoulomb-switch = 0 vdw-type = Cut-off ; truncation for minimisation, with large cutoff rvdw-switch = 0 rvdw = 0 ; cut-off lengths epsilon_surface = 0 optimize_fft = yes Tcoupl = V-rescale tc_grps = system tau_t = 0.01 ref_t = 300 Pcoupl = no ; Parrinello-Rahman ; Pressure coupling gen_vel = yes gen_temp= 300 gen_seed= -1 constraints = none ; OPTIONS FOR BOND CONSTRAINTS constraint-algorithm = Lincs ; Type of constraint algorithm lincs_order = 4;4; Highest order in the expansion of the constraint coupling matrix lincs_iter = 1 lincs_warnangle = 30 ; Lincs will write a warning to the stderr if in one step a bond rotates ; over more degrees than unconstrained-start = no ; Do not constrain the start configuration ;Shake-SOR= no ; Use successive overrelaxation to reduce the number of shake iterations ;shake-tol= 1e-04 ; Relative tolerance of shake morse= no ; Convert harmonic bonds to morse potentials / *Could you please have a check for me again? Thanks in advance! All the best, Qinghua* -- View this message in context: http://gromacs.5086.x6.nabble.com/single-point-calculation-with-gromacs-tp5012084p5012100.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list
[gmx-users] Re: single point calculation with gromacs
Dear Justin, *Thanks very much for your reply! Here is my minim.mdp I used:* /; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 0 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) rlist = 9.0 ; Cut-off for making neighbor list (short range forces) coulombtype = Cut-off ; Treatment of long range electrostatic interactions rcoulomb= 9.0 ; Short-range electrostatic cut-off rvdw= 9.0 ; Short-range Van der Waals cut-off pbc = no; Periodic Boundary Conditions (yes/no) / *If I used this mdp file for 0-step minimization, I could get potential energy around 700 kJ/mol for my system. But I would get potential energy around 2.6e+05 kJ/mol if I used the mdv.mdp (md simulation in vacuum) for calculations with rerun option. And the bond potential could also reach as high as 1.1e+05 kJ/mol. Actually, my system is very small, it contains only 37 atoms. I believe that the energy reported by 0-step minimization were more reasonable. So I guess that there might be some problem for the mdp file usd with rerun, and here is the mdv.mdp:* /define = ;-DPOSRES integrator = md ; molecular dynamics algorithm tinit = 0.0 ; start time and timestep in ps dt = 0.002; time step in ps nsteps = 2; number of steps for 1000ns run emtol = 100; convergence criterion emstep = 0.05 ; intial step size nstlist = 0 ; step frequency for updating neighbour list ns_type = simple ; method for neighbour searching (?) nstxout = 1; frequency for writing coords to output .trr file nstvout = 1 ; frequency for writing velocities to output...should be same as nstxout nstfout = 1; frequency for writing forces to output nstlog = 1 ; frequency for writing energies to log file nstenergy = 1 ; frequency for writing energies to energy file nstxtcout = 1 ; frequency for writing coords to xtc traj xtc_grps= system ; group(s) whose coords are to be written in xtc traj energygrps = system ; group(s) whose energy is to be written in energy file pbc = no ; use pbc rlist = 0 ; cutoff lengths (nm) epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range or DC of reaction field niter = 100 ; Some thingies for future use fourierspacing = 0.16 fourier_nx = 30 fourier_ny = 30 fourier_nz = 30 coulombtype = Cut-off ; truncation for minimisation, with large cutoff rcoulomb= 0 rcoulomb-switch = 0 vdw-type = Cut-off ; truncation for minimisation, with large cutoff rvdw-switch = 0 rvdw = 0 ; cut-off lengths epsilon_surface = 0 optimize_fft = yes Tcoupl = V-rescale tc_grps = system tau_t = 0.01 ref_t = 300 Pcoupl = no ; Parrinello-Rahman ; Pressure coupling gen_vel = yes gen_temp= 300 gen_seed= -1 constraints = none ; OPTIONS FOR BOND CONSTRAINTS constraint-algorithm = Lincs ; Type of constraint algorithm lincs_order = 4;4; Highest order in the expansion of the constraint coupling matrix lincs_iter = 1 lincs_warnangle = 30 ; Lincs will write a warning to the stderr if in one step a bond rotates ; over more degrees than unconstrained-start = no ; Do not constrain the start configuration ;Shake-SOR= no ; Use successive overrelaxation to reduce the number of shake iterations ;shake-tol= 1e-04 ; Relative tolerance of shake morse= no ; Convert harmonic bonds to morse potentials / *Could you please have a check for me again? Thanks in advance! All the best, Qinghua* -- View this message in context: http://gromacs.5086.x6.nabble.com/single-point-calculation-with-gromacs-tp5012084p5012101.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list
Re: [gmx-users] Re: single point calculation with gromacs
On 10/31/13 4:57 AM, fantasticqhl wrote: Dear Justin, *Thanks very much for your reply! Here is my minim.mdp I used:* /; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 0 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) rlist = 9.0 ; Cut-off for making neighbor list (short range forces) coulombtype = Cut-off ; Treatment of long range electrostatic interactions rcoulomb= 9.0 ; Short-range electrostatic cut-off rvdw= 9.0 ; Short-range Van der Waals cut-off pbc = no; Periodic Boundary Conditions (yes/no) / *If I used this mdp file for 0-step minimization, I could get potential energy around 700 kJ/mol for my system. But I would get potential energy around 2.6e+05 kJ/mol if I used the mdv.mdp (md simulation in vacuum) for calculations with rerun option. And the bond potential could also reach as high as 1.1e+05 kJ/mol. Actually, my system is very small, it contains only 37 atoms. I believe that the energy reported by 0-step minimization were more reasonable. So I guess that there might be some problem for the mdp file usd with rerun, and here is the mdv.mdp:* /define = ;-DPOSRES integrator = md ; molecular dynamics algorithm tinit = 0.0 ; start time and timestep in ps dt = 0.002; time step in ps nsteps = 2; number of steps for 1000ns run emtol = 100; convergence criterion emstep = 0.05 ; intial step size nstlist = 0 ; step frequency for updating neighbour list ns_type = simple ; method for neighbour searching (?) nstxout = 1; frequency for writing coords to output .trr file nstvout = 1 ; frequency for writing velocities to output...should be same as nstxout nstfout = 1; frequency for writing forces to output nstlog = 1 ; frequency for writing energies to log file nstenergy = 1 ; frequency for writing energies to energy file nstxtcout = 1 ; frequency for writing coords to xtc traj xtc_grps= system ; group(s) whose coords are to be written in xtc traj energygrps = system ; group(s) whose energy is to be written in energy file pbc = no ; use pbc rlist = 0 ; cutoff lengths (nm) epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range or DC of reaction field niter = 100 ; Some thingies for future use fourierspacing = 0.16 fourier_nx = 30 fourier_ny = 30 fourier_nz = 30 coulombtype = Cut-off ; truncation for minimisation, with large cutoff rcoulomb= 0 rcoulomb-switch = 0 vdw-type = Cut-off ; truncation for minimisation, with large cutoff rvdw-switch = 0 rvdw = 0 ; cut-off lengths epsilon_surface = 0 optimize_fft = yes Tcoupl = V-rescale tc_grps = system tau_t = 0.01 ref_t = 300 Pcoupl = no ; Parrinello-Rahman ; Pressure coupling gen_vel = yes gen_temp= 300 gen_seed= -1 constraints = none ; OPTIONS FOR BOND CONSTRAINTS constraint-algorithm = Lincs ; Type of constraint algorithm lincs_order = 4;4; Highest order in the expansion of the constraint coupling matrix lincs_iter = 1 lincs_warnangle = 30 ; Lincs will write a warning to the stderr if in one step a bond rotates ; over more degrees than unconstrained-start = no ; Do not constrain the start configuration ;Shake-SOR= no ; Use successive overrelaxation to reduce the number of shake iterations ;shake-tol= 1e-04 ; Relative tolerance of shake morse= no ; Convert harmonic bonds to morse potentials / *Could you please have a check for me again? Thanks in advance! Was anything in the bug report I posted before relevant? If you're using any version in the 4.6.x series, you may be observing some of the same behavior I did. There are numerous differences between these .mdp
