Re: [gmx-users] Energy Minimization Error
Dear Gromacs users, When I tried to run the equilibration run, it gave several LINCS WARNINGS. However, that equilibration run is completed by the Gromacs. Do I have to concern about these warnings or can I ignore those? Thank you. Sincerely, A. Guruge On Fri, Oct 20, 2017 at 11:22 AM, Justin Lemkul wrote: > > > On 10/19/17 8:21 PM, Amali Guruge wrote: > >> Dear Gromacs users, >> >> Thank you very much for the reply. My concern is "step 11: One or more >> water molecules can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate". What >> should I do to avoid it? >> > > That happens often during minimization, especially the early steps. If it > doesn't come back up again, it's fine. It should never happen during MD. > > -Justin > > > Thank you. >> >> On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul wrote: >> >> >>> On 10/19/17 8:10 PM, Amali Guruge wrote: >>> >>> Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= 14611 Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= 18527 Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= 1005 Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= 6994 Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= 58902 Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= 515 Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= 188631 Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= 188631 Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= 188631 Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= 188631 Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= 188631 step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. After 2000 steps it says, Steepest Descents did not converge to Fmax < 500 in 2001 steps. Potential Energy = -4.6310655e+06 Maximum force = 6.7453154e+03 on atom 18769 Norm of force = 3.3632809e+01 Simulation ended prematurely, no performance report will be written. my em.mdp file contains following parameters. integrator= steep; simulation algorithm dt= 0.002; time step (ps) nsteps= 2000; # steps comm_mode= linear; c.o.m. motion reset ; ;Energy Minimization emtol= 500; converged F lt value (kJ mol-1 nm-1) emstep= 0.01 ; initial step size (nm) ; ;Output Control nstxout= 5 ; write coordinates to .trr nstvout= 5; write velocities to .trr nstlog= 5; write energies to .log nstenergy= 1; write energies to .edr ; ;Neightbour Searching cutoff-scheme = Verlet; scheme used for generating pair list nstlist = 10 ; update neighbour list ns_type= grid; neighbour list method pbc= xyz; periodic boundary conditions rlist= 0.9 ; cut-off for short-range neighbour (nm) ; ;Electrostatics and VdW coulombtype= PME; type of coulomb interaction rcoulomb= 0.9; cut-off distance for coulomb epsilon_r= 1; dielectric constant rvdw= 0.9; cut-off for vdw fourierspacing= 0.12; maximum grid spacing for FFT pme_order= 4; interpolation order for PME ewald_rtol= 1e-5; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ;Temperature Coupling Tcoupl= no; type of temperature coupling ; ;Pressure Coupling Pcoupl= no ; type of pressure coupling ; ;Velocity Generation gen_vel= no ; generate initial velocities ; ;Bonds constraints= none; bond constraint type I used gmx solvate to add water molecules to the system.
Re: [gmx-users] Energy Minimization Error
On 10/19/17 8:21 PM, Amali Guruge wrote: Dear Gromacs users, Thank you very much for the reply. My concern is "step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate". What should I do to avoid it? That happens often during minimization, especially the early steps. If it doesn't come back up again, it's fine. It should never happen during MD. -Justin Thank you. On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul wrote: On 10/19/17 8:10 PM, Amali Guruge wrote: Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= 14611 Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= 18527 Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= 1005 Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= 6994 Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= 58902 Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= 515 Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= 188631 Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= 188631 Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= 188631 Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= 188631 Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= 188631 step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. After 2000 steps it says, Steepest Descents did not converge to Fmax < 500 in 2001 steps. Potential Energy = -4.6310655e+06 Maximum force = 6.7453154e+03 on atom 18769 Norm of force = 3.3632809e+01 Simulation ended prematurely, no performance report will be written. my em.mdp file contains following parameters. integrator= steep; simulation algorithm dt= 0.002; time step (ps) nsteps= 2000; # steps comm_mode= linear; c.o.m. motion reset ; ;Energy Minimization emtol= 500; converged F lt value (kJ mol-1 nm-1) emstep= 0.01 ; initial step size (nm) ; ;Output Control nstxout= 5 ; write coordinates to .trr nstvout= 5; write velocities to .trr nstlog= 5; write energies to .log nstenergy= 1; write energies to .edr ; ;Neightbour Searching cutoff-scheme = Verlet; scheme used for generating pair list nstlist = 10 ; update neighbour list ns_type= grid; neighbour list method pbc= xyz; periodic boundary conditions rlist= 0.9 ; cut-off for short-range neighbour (nm) ; ;Electrostatics and VdW coulombtype= PME; type of coulomb interaction rcoulomb= 0.9; cut-off distance for coulomb epsilon_r= 1; dielectric constant rvdw= 0.9; cut-off for vdw fourierspacing= 0.12; maximum grid spacing for FFT pme_order= 4; interpolation order for PME ewald_rtol= 1e-5; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ;Temperature Coupling Tcoupl= no; type of temperature coupling ; ;Pressure Coupling Pcoupl= no ; type of pressure coupling ; ;Velocity Generation gen_vel= no ; generate initial velocities ; ;Bonds constraints= none; bond constraint type I used gmx solvate to add water molecules to the system. How could I get rid of bad contacts of water molecules? Appreciate if anyone help me to solve the problem. mdrun stopped after 2000 steps because you told it to. You need to minimize further, so increase nsteps (or set it to -1 to let mdrun go as long as it needs to without having to guess a number). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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 ht
Re: [gmx-users] Energy Minimization Error
Dear Gromacs users, Thank you very much for the reply. My concern is "step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate". What should I do to avoid it? Thank you. On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul wrote: > > > On 10/19/17 8:10 PM, Amali Guruge wrote: > >> Dear Gromacs Users, >> >> I tried to energy minimize my system using the steep integrator. However, >> it gave the following message. >> >> Steepest Descents: >> Tolerance (Fmax) = 5.0e+02 >> Number of steps= 2000 >> Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= >> 14611 >> Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= >> 18527 >> Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= >> 1005 >> Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= >> 6994 >> Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= >> 58902 >> Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= >> 515 >> Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= >> 188631 >> Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= >> 188631 >> Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= >> 188631 >> Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= >> 188631 >> Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= >> 188631 >> >> step 11: One or more water molecules can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> >> After 2000 steps it says, >> >> Steepest Descents did not converge to Fmax < 500 in 2001 steps. >> Potential Energy = -4.6310655e+06 >> Maximum force = 6.7453154e+03 on atom 18769 >> Norm of force = 3.3632809e+01 >> >> Simulation ended prematurely, no performance report will be written. >> >> >> my em.mdp file contains following parameters. >> >> integrator= steep; simulation algorithm >> dt= 0.002; time step (ps) >> nsteps= 2000; # steps >> comm_mode= linear; c.o.m. motion reset >> ; >> ;Energy Minimization >> emtol= 500; converged F lt value (kJ mol-1 nm-1) >> emstep= 0.01 ; initial step size (nm) >> ; >> ;Output Control >> nstxout= 5 ; write coordinates to .trr >> nstvout= 5; write velocities to .trr >> nstlog= 5; write energies to .log >> nstenergy= 1; write energies to .edr >> ; >> ;Neightbour Searching >> cutoff-scheme = Verlet; scheme used for >> generating pair list >> nstlist = 10 ; update neighbour list >> ns_type= grid; neighbour list method >> pbc= xyz; periodic boundary conditions >> rlist= 0.9 ; cut-off for short-range neighbour >> (nm) >> ; >> ;Electrostatics and VdW >> coulombtype= PME; type of coulomb interaction >> rcoulomb= 0.9; cut-off distance for coulomb >> epsilon_r= 1; dielectric constant >> rvdw= 0.9; cut-off for vdw >> fourierspacing= 0.12; maximum grid spacing for FFT >> pme_order= 4; interpolation order for PME >> ewald_rtol= 1e-5; relative strength of Ewald-shifted >> DispCorr= EnerPres ; long range dispersion >> corrections >> ; >> ;Temperature Coupling >> Tcoupl= no; type of temperature coupling >> ; >> ;Pressure Coupling >> Pcoupl= no ; type of pressure coupling >> ; >> ;Velocity Generation >> gen_vel= no ; generate initial velocities >> ; >> ;Bonds >> constraints= none; bond constraint type >> >> I used gmx solvate to add water molecules to the system. >> >> How could I get rid of bad contacts of water molecules? Appreciate if >> anyone help me to solve the problem. >> > > mdrun stopped after 2000 steps because you told it to. You need to > minimize further, so increase nsteps (or set it to -1 to let mdrun go as > long as it needs to without having to guess a number). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users
Re: [gmx-users] Energy Minimization Error
On 10/19/17 8:10 PM, Amali Guruge wrote: Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= 14611 Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= 18527 Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= 1005 Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= 6994 Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= 58902 Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= 515 Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= 188631 Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= 188631 Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= 188631 Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= 188631 Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= 188631 step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. After 2000 steps it says, Steepest Descents did not converge to Fmax < 500 in 2001 steps. Potential Energy = -4.6310655e+06 Maximum force = 6.7453154e+03 on atom 18769 Norm of force = 3.3632809e+01 Simulation ended prematurely, no performance report will be written. my em.mdp file contains following parameters. integrator= steep; simulation algorithm dt= 0.002; time step (ps) nsteps= 2000; # steps comm_mode= linear; c.o.m. motion reset ; ;Energy Minimization emtol= 500; converged F lt value (kJ mol-1 nm-1) emstep= 0.01 ; initial step size (nm) ; ;Output Control nstxout= 5 ; write coordinates to .trr nstvout= 5; write velocities to .trr nstlog= 5; write energies to .log nstenergy= 1; write energies to .edr ; ;Neightbour Searching cutoff-scheme = Verlet; scheme used for generating pair list nstlist = 10 ; update neighbour list ns_type= grid; neighbour list method pbc= xyz; periodic boundary conditions rlist= 0.9 ; cut-off for short-range neighbour (nm) ; ;Electrostatics and VdW coulombtype= PME; type of coulomb interaction rcoulomb= 0.9; cut-off distance for coulomb epsilon_r= 1; dielectric constant rvdw= 0.9; cut-off for vdw fourierspacing= 0.12; maximum grid spacing for FFT pme_order= 4; interpolation order for PME ewald_rtol= 1e-5; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ;Temperature Coupling Tcoupl= no; type of temperature coupling ; ;Pressure Coupling Pcoupl= no ; type of pressure coupling ; ;Velocity Generation gen_vel= no ; generate initial velocities ; ;Bonds constraints= none; bond constraint type I used gmx solvate to add water molecules to the system. How could I get rid of bad contacts of water molecules? Appreciate if anyone help me to solve the problem. mdrun stopped after 2000 steps because you told it to. You need to minimize further, so increase nsteps (or set it to -1 to let mdrun go as long as it needs to without having to guess a number). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Energy Minimization Error
Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= 14611 Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= 18527 Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= 1005 Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= 6994 Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= 58902 Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= 515 Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= 188631 Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= 188631 Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= 188631 Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= 188631 Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= 188631 step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. After 2000 steps it says, Steepest Descents did not converge to Fmax < 500 in 2001 steps. Potential Energy = -4.6310655e+06 Maximum force = 6.7453154e+03 on atom 18769 Norm of force = 3.3632809e+01 Simulation ended prematurely, no performance report will be written. my em.mdp file contains following parameters. integrator= steep; simulation algorithm dt= 0.002; time step (ps) nsteps= 2000; # steps comm_mode= linear; c.o.m. motion reset ; ;Energy Minimization emtol= 500; converged F lt value (kJ mol-1 nm-1) emstep= 0.01 ; initial step size (nm) ; ;Output Control nstxout= 5 ; write coordinates to .trr nstvout= 5; write velocities to .trr nstlog= 5; write energies to .log nstenergy= 1; write energies to .edr ; ;Neightbour Searching cutoff-scheme = Verlet; scheme used for generating pair list nstlist = 10 ; update neighbour list ns_type= grid; neighbour list method pbc= xyz; periodic boundary conditions rlist= 0.9 ; cut-off for short-range neighbour (nm) ; ;Electrostatics and VdW coulombtype= PME; type of coulomb interaction rcoulomb= 0.9; cut-off distance for coulomb epsilon_r= 1; dielectric constant rvdw= 0.9; cut-off for vdw fourierspacing= 0.12; maximum grid spacing for FFT pme_order= 4; interpolation order for PME ewald_rtol= 1e-5; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ;Temperature Coupling Tcoupl= no; type of temperature coupling ; ;Pressure Coupling Pcoupl= no ; type of pressure coupling ; ;Velocity Generation gen_vel= no ; generate initial velocities ; ;Bonds constraints= none; bond constraint type I used gmx solvate to add water molecules to the system. How could I get rid of bad contacts of water molecules? Appreciate if anyone help me to solve the problem. Thank you. Sincerely, A Guruge -- 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] energy minimization error
Hi, pdb2gmx and grompp are pretty talkative about things like missing parameters and bonds - go back and read what they had to say, and particularly what pdb2gmx thought about your specbonds. Mark On Fri, Oct 23, 2015 at 5:51 PM faride badalkhani wrote: > Hi, > > Thanks a lot for your time and patience. This time, I chose a very simple > structure and then inspected the generated topology. The interesting point > was that, there were some missing interactions. When I inspected them. I > found that I had defined those interactions in ffbonded.itp file, but > pdb2gmx has not assigned those definitions to these interactions. However, > I added the appropriate gb_, ga_, or gd_ manually, and then performed the > MD simulations and received an error as follows: > > Step= 210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom= > 46 > Step= 212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom= > 44 > Step= 216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom= > 46 > Step= 218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom= > 44 > Step= 221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom= > 46 > Step= 224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom= > 44 > Step= 227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom= > 46 > Step= 229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom= > 44 > Step= 232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom= > 46 > Step= 234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom= > 44 > Step= 235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom= > 46 > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 100 (which may not be possible for your system). > It stopped because the algorithm tried to make a new step whose size was > too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 236 steps, > but did not reach the requested Fmax < 100. > Potential Energy = -8.9157188e+04 > Maximum force = 1.7089320e+05 on atom 44 > Norm of force = 3.3110510e+03 > > gcq#220: "Let's Go Hang Out In a Mall" (LIVE) > > farideh@farideh-P61A-D3:~/multiple/G0$ > > you can access all the files via the following link: > https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0 > > Truly yours, > Farideh > > On Thu, Oct 22, 2015 at 11:24 AM, Mark Abraham > wrote: > > > Hi, > > > > Did you inspect your topology like I suggested? You need to know that > there > > are bonds exactly where you intend them, before doing any calculations > with > > them. > > > > Mark > > > > On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani < > > farideh.kham...@gmail.com> > > wrote: > > > > > Hi, > > > > > > I am trying to simulate a hyper-branched polymer (a dendrimer) in > water. > > > But, every time the system blows up at energy minimization step. > > Therefore, > > > according to what Mark had recommended I decided to start with a much > > > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I > had > > > optimized it at M062x/6-31G* level, before starting the MD simulations. > > > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it > > > residue by residue. After that, I started simulation procedure and > > > continued step by step. In spite of G3 PAMAM dendrimer I didn't face > any > > > errors in energy minimization step, and the potential energy - EM step > > plot > > > was reasonable. But, when I loaded em.gro file in VMD, the structure > was > > > completely messed up as in G3 dendrimer. This time I continued the MD > > > simulation until production MD, and there was no error. However, the > > system > > > is blown up. You can access all the simulation files, pdb structure, > and > > > the photos of G1 structure before and after EM step via: > > > > > > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0 > > > > > > Since I am a beginner in this area, I do not know what is the solution > > for > > > this problem. > > > Do you think errors that occur during the G3 simulation are relevant to > > the > > > initial structure? > > > any suggestion or recommendation is appreciated. > > > > > > Thanks in advance > > > Farideh > > > -- > > > 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/Mailin
Re: [gmx-users] energy minimization error
Hi, Thanks a lot for your time and patience. This time, I chose a very simple structure and then inspected the generated topology. The interesting point was that, there were some missing interactions. When I inspected them. I found that I had defined those interactions in ffbonded.itp file, but pdb2gmx has not assigned those definitions to these interactions. However, I added the appropriate gb_, ga_, or gd_ manually, and then performed the MD simulations and received an error as follows: Step= 210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom= 46 Step= 212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom= 44 Step= 216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom= 46 Step= 218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom= 44 Step= 221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom= 46 Step= 224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom= 44 Step= 227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom= 46 Step= 229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom= 44 Step= 232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom= 46 Step= 234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom= 44 Step= 235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom= 46 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 100 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 236 steps, but did not reach the requested Fmax < 100. Potential Energy = -8.9157188e+04 Maximum force = 1.7089320e+05 on atom 44 Norm of force = 3.3110510e+03 gcq#220: "Let's Go Hang Out In a Mall" (LIVE) farideh@farideh-P61A-D3:~/multiple/G0$ you can access all the files via the following link: https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0 Truly yours, Farideh On Thu, Oct 22, 2015 at 11:24 AM, Mark Abraham wrote: > Hi, > > Did you inspect your topology like I suggested? You need to know that there > are bonds exactly where you intend them, before doing any calculations with > them. > > Mark > > On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani < > farideh.kham...@gmail.com> > wrote: > > > Hi, > > > > I am trying to simulate a hyper-branched polymer (a dendrimer) in water. > > But, every time the system blows up at energy minimization step. > Therefore, > > according to what Mark had recommended I decided to start with a much > > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had > > optimized it at M062x/6-31G* level, before starting the MD simulations. > > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it > > residue by residue. After that, I started simulation procedure and > > continued step by step. In spite of G3 PAMAM dendrimer I didn't face any > > errors in energy minimization step, and the potential energy - EM step > plot > > was reasonable. But, when I loaded em.gro file in VMD, the structure was > > completely messed up as in G3 dendrimer. This time I continued the MD > > simulation until production MD, and there was no error. However, the > system > > is blown up. You can access all the simulation files, pdb structure, and > > the photos of G1 structure before and after EM step via: > > > > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0 > > > > Since I am a beginner in this area, I do not know what is the solution > for > > this problem. > > Do you think errors that occur during the G3 simulation are relevant to > the > > initial structure? > > any suggestion or recommendation is appreciated. > > > > Thanks in advance > > Farideh > > -- > > 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-
Re: [gmx-users] energy minimization error
Hi, Did you inspect your topology like I suggested? You need to know that there are bonds exactly where you intend them, before doing any calculations with them. Mark On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani wrote: > Hi, > > I am trying to simulate a hyper-branched polymer (a dendrimer) in water. > But, every time the system blows up at energy minimization step. Therefore, > according to what Mark had recommended I decided to start with a much > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had > optimized it at M062x/6-31G* level, before starting the MD simulations. > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it > residue by residue. After that, I started simulation procedure and > continued step by step. In spite of G3 PAMAM dendrimer I didn't face any > errors in energy minimization step, and the potential energy - EM step plot > was reasonable. But, when I loaded em.gro file in VMD, the structure was > completely messed up as in G3 dendrimer. This time I continued the MD > simulation until production MD, and there was no error. However, the system > is blown up. You can access all the simulation files, pdb structure, and > the photos of G1 structure before and after EM step via: > > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0 > > Since I am a beginner in this area, I do not know what is the solution for > this problem. > Do you think errors that occur during the G3 simulation are relevant to the > initial structure? > any suggestion or recommendation is appreciated. > > Thanks in advance > Farideh > -- > 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] energy minimization error
Hi, I am trying to simulate a hyper-branched polymer (a dendrimer) in water. But, every time the system blows up at energy minimization step. Therefore, according to what Mark had recommended I decided to start with a much smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had optimized it at M062x/6-31G* level, before starting the MD simulations. Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it residue by residue. After that, I started simulation procedure and continued step by step. In spite of G3 PAMAM dendrimer I didn't face any errors in energy minimization step, and the potential energy - EM step plot was reasonable. But, when I loaded em.gro file in VMD, the structure was completely messed up as in G3 dendrimer. This time I continued the MD simulation until production MD, and there was no error. However, the system is blown up. You can access all the simulation files, pdb structure, and the photos of G1 structure before and after EM step via: https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0 Since I am a beginner in this area, I do not know what is the solution for this problem. Do you think errors that occur during the G3 simulation are relevant to the initial structure? any suggestion or recommendation is appreciated. Thanks in advance Farideh -- 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] Energy minimization error
Hi, As you said, I started with a G1 PAMAM dendrimer, rather than a G3 one. I had optimized it at M062x/6-31G* level, before starting the MD simulations. Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it residue by residue. After that, I started simulation procedure and continued step by step. In spite of G3 PAMAM dendrimer I didn't face any errors in energy minimization step, and the potential energy - EM step plot was reasonable. But, when I loaded em.gro file in VMD, the structure was completely messed up as in G3 dendrimer. This time I continued the MD simulation until production MD, and there was no error. However, the system is blown up. You can access all the simulation files, pdb structure, and the photos of G1 structure before and after EM step via: https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0 Since I am a beginner in this area, I do not know what is the solution for this problem. Do you think errors that occur during the G3 simulation are relevant to the initial structure? any suggestion or recommendation is appreciated. Thanks in advance Farideh On Sat, Oct 17, 2015 at 6:29 PM, Mark Abraham wrote: > Hi, > > What some visualization program shows about bonds doesn't mean anything - > it has not parsed your topology. You have no option but to look at the .top > produced and reason about what it shows, but yours is very complex. I > strongly recommend starting with something simpler than a multiply branched > dendrimer. Join two units with a specbond, inspect the .top so that you > know it has what you think it has, and get that to EM and simulation > stably. Then you can get more complex. > > Mark > > On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani < > farideh.kham...@gmail.com> > wrote: > > > Dear gromacs users, > > > > As I said before I faced with the minimization error, so I changed > > coordinates of atoms in pdb file, but the problem is the same. the only > > thing that changes in every run is atom number. I modified pdb for many > > times. > > > > Steepest Descents converged to Fmax < 1000 in 530 steps > > Potential Energy = -5.5180181e+05 > > Maximum force = 7.4496063e+02 on atom 501 > > Norm of force = 3.8248455e+01 > > > > > > Moreover gro structure was completely messed up when was visualized in > vmd. > > you can see the picture of my structure in below dropbox link: > > > > https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0 > > https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0 > > > > and this is the pdb file dropbox link: > > > > https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0 > > > > > > I used cg algorithm after steep for minimization, too. But it did not > work. > > is there any way to solve this problem? > > > > any help is appreciated. > > > > On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham > > wrote: > > > > > Hi, > > > > > > Look at atom 380 and see why the forces might be high. > > > > > > Mark > > > > > > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani < > > > farideh.kham...@gmail.com> > > > wrote: > > > > > > > Thank you for your great help on specbond.dat file. I defined it and > I > > > > could go ahead until Energy minimization step. I have used this > > minim.mdp > > > > file > > > > > > > > ; 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= 5 ; 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 = grid; Method to determine neighbor list > > > > (simple, grid) > > > > rlist = 1.0; Cut-off for making neighbor list > > > > (short range forces) > > > > coulombtype= PME; Treatment of long range electrostatic > > > > interactions > > > > rcoulomb = 1.0; Short-range electrostatic cut-off > > > > rvdw = 1.0; Short-range Van der Waals cut-off > > > > pbc = xyz ; Periodic Boundary Conditions > > (yes/no) > > > > > > > > But when I run mdrun -v -deffnm em command, 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). > > > > It stopped because the algorithm tried to make a new step whose size > > was > > > > too > > > > small, or there was no change in the energy since last step. Either > > way, > > > w
Re: [gmx-users] Energy minimization error
Hi, What some visualization program shows about bonds doesn't mean anything - it has not parsed your topology. You have no option but to look at the .top produced and reason about what it shows, but yours is very complex. I strongly recommend starting with something simpler than a multiply branched dendrimer. Join two units with a specbond, inspect the .top so that you know it has what you think it has, and get that to EM and simulation stably. Then you can get more complex. Mark On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani wrote: > Dear gromacs users, > > As I said before I faced with the minimization error, so I changed > coordinates of atoms in pdb file, but the problem is the same. the only > thing that changes in every run is atom number. I modified pdb for many > times. > > Steepest Descents converged to Fmax < 1000 in 530 steps > Potential Energy = -5.5180181e+05 > Maximum force = 7.4496063e+02 on atom 501 > Norm of force = 3.8248455e+01 > > > Moreover gro structure was completely messed up when was visualized in vmd. > you can see the picture of my structure in below dropbox link: > > https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0 > https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0 > > and this is the pdb file dropbox link: > > https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0 > > > I used cg algorithm after steep for minimization, too. But it did not work. > is there any way to solve this problem? > > any help is appreciated. > > On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham > wrote: > > > Hi, > > > > Look at atom 380 and see why the forces might be high. > > > > Mark > > > > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani < > > farideh.kham...@gmail.com> > > wrote: > > > > > Thank you for your great help on specbond.dat file. I defined it and I > > > could go ahead until Energy minimization step. I have used this > minim.mdp > > > file > > > > > > ; 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= 5 ; 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 = grid; Method to determine neighbor list > > > (simple, grid) > > > rlist = 1.0; Cut-off for making neighbor list > > > (short range forces) > > > coulombtype= PME; Treatment of long range electrostatic > > > interactions > > > rcoulomb = 1.0; Short-range electrostatic cut-off > > > rvdw = 1.0; Short-range Van der Waals cut-off > > > pbc = xyz ; Periodic Boundary Conditions > (yes/no) > > > > > > But when I run mdrun -v -deffnm em command, 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). > > > It stopped because the algorithm tried to make a new step whose size > was > > > too > > > small, or there was no change in the energy since last step. Either > way, > > we > > > regard the minimization as converged to within the available machine > > > precision, given your starting configuration and EM parameters. > > > > > > Double precision normally gives you higher accuracy, but this is often > > not > > > needed for preparing to run molecular dynamics. > > > You might need to increase your constraint accuracy, or turn > > > off constraints altogether (set constraints = none in mdp file) > > > > > > writing lowest energy coordinates. > > > > > > Steepest Descents converged to machine precision in 90 steps, > > > but did not reach the requested Fmax < 1000. > > > Potential Energy = -2.3956744e+05 > > > Maximum force = 1.5824519e+05 on atom 380 > > > Norm of force = 1.7695243e+03 > > > > > > gcq#187: "Been There, Done It" (Beavis and Butthead) > > > > > > farideh@farideh-P61A-D3:~/FARIDEH$ > > > > > > I changed the emtol, emstep, and nsteps for a few times. However, I > > > couldn't resolve this problem. Could you tell me if there is something > > > wrong with the minim.mdp file? > > > > > > You can see all the files via: > > > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 > > > > > > Truly yours, > > > Farideh > > > -- > > > 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.grom
Re: [gmx-users] Energy minimization error
Dear gromacs users, As I said before I faced with the minimization error, so I changed coordinates of atoms in pdb file, but the problem is the same. the only thing that changes in every run is atom number. I modified pdb for many times. Steepest Descents converged to Fmax < 1000 in 530 steps Potential Energy = -5.5180181e+05 Maximum force = 7.4496063e+02 on atom 501 Norm of force = 3.8248455e+01 Moreover gro structure was completely messed up when was visualized in vmd. you can see the picture of my structure in below dropbox link: https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0 https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0 and this is the pdb file dropbox link: https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0 I used cg algorithm after steep for minimization, too. But it did not work. is there any way to solve this problem? any help is appreciated. On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham wrote: > Hi, > > Look at atom 380 and see why the forces might be high. > > Mark > > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani < > farideh.kham...@gmail.com> > wrote: > > > Thank you for your great help on specbond.dat file. I defined it and I > > could go ahead until Energy minimization step. I have used this minim.mdp > > file > > > > ; 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= 5 ; 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 = grid; Method to determine neighbor list > > (simple, grid) > > rlist = 1.0; Cut-off for making neighbor list > > (short range forces) > > coulombtype= PME; Treatment of long range electrostatic > > interactions > > rcoulomb = 1.0; Short-range electrostatic cut-off > > rvdw = 1.0; Short-range Van der Waals cut-off > > pbc = xyz ; Periodic Boundary Conditions (yes/no) > > > > But when I run mdrun -v -deffnm em command, 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). > > It stopped because the algorithm tried to make a new step whose size was > > too > > small, or there was no change in the energy since last step. Either way, > we > > regard the minimization as converged to within the available machine > > precision, given your starting configuration and EM parameters. > > > > Double precision normally gives you higher accuracy, but this is often > not > > needed for preparing to run molecular dynamics. > > You might need to increase your constraint accuracy, or turn > > off constraints altogether (set constraints = none in mdp file) > > > > writing lowest energy coordinates. > > > > Steepest Descents converged to machine precision in 90 steps, > > but did not reach the requested Fmax < 1000. > > Potential Energy = -2.3956744e+05 > > Maximum force = 1.5824519e+05 on atom 380 > > Norm of force = 1.7695243e+03 > > > > gcq#187: "Been There, Done It" (Beavis and Butthead) > > > > farideh@farideh-P61A-D3:~/FARIDEH$ > > > > I changed the emtol, emstep, and nsteps for a few times. However, I > > couldn't resolve this problem. Could you tell me if there is something > > wrong with the minim.mdp file? > > > > You can see all the files via: > > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 > > > > Truly yours, > > Farideh > > -- > > 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. > -- 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 *
Re: [gmx-users] Energy minimization error
Hi, Look at atom 380 and see why the forces might be high. Mark On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani wrote: > Thank you for your great help on specbond.dat file. I defined it and I > could go ahead until Energy minimization step. I have used this minim.mdp > file > > ; 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= 5 ; 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 = grid; Method to determine neighbor list > (simple, grid) > rlist = 1.0; Cut-off for making neighbor list > (short range forces) > coulombtype= PME; Treatment of long range electrostatic > interactions > rcoulomb = 1.0; Short-range electrostatic cut-off > rvdw = 1.0; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions (yes/no) > > But when I run mdrun -v -deffnm em command, 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). > It stopped because the algorithm tried to make a new step whose size was > too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 90 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -2.3956744e+05 > Maximum force = 1.5824519e+05 on atom 380 > Norm of force = 1.7695243e+03 > > gcq#187: "Been There, Done It" (Beavis and Butthead) > > farideh@farideh-P61A-D3:~/FARIDEH$ > > I changed the emtol, emstep, and nsteps for a few times. However, I > couldn't resolve this problem. Could you tell me if there is something > wrong with the minim.mdp file? > > You can see all the files via: > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 > > Truly yours, > Farideh > -- > 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] Energy minimization error
Thank you for your great help on specbond.dat file. I defined it and I could go ahead until Energy minimization step. I have used this minim.mdp file ; 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= 5 ; 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 = grid; Method to determine neighbor list (simple, grid) rlist = 1.0; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb = 1.0; Short-range electrostatic cut-off rvdw = 1.0; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) But when I run mdrun -v -deffnm em command, 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). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 90 steps, but did not reach the requested Fmax < 1000. Potential Energy = -2.3956744e+05 Maximum force = 1.5824519e+05 on atom 380 Norm of force = 1.7695243e+03 gcq#187: "Been There, Done It" (Beavis and Butthead) farideh@farideh-P61A-D3:~/FARIDEH$ I changed the emtol, emstep, and nsteps for a few times. However, I couldn't resolve this problem. Could you tell me if there is something wrong with the minim.mdp file? You can see all the files via: https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 Truly yours, Farideh -- 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] energy minimization error
On 6/27/15 2:29 AM, James Lord wrote: Hi Justin For now I used *mdrun -nt 1* * and got rid of this error so hopefully the simulation wont crash. * The DD errors have nothing to do with physical stability; you just can't necessarily parallelize any arbitrary system over any arbitrary number of cores (DD cells). You can also parallelize with OpenMP to get some speed-up (mdrun -ntmpi 1 -ntomp N). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] energy minimization error
Hi Justin For now I used *mdrun -nt 1* * and got rid of this error so hopefully the simulation wont crash. * *Cheers* *James* On Sat, Jun 27, 2015 at 11:19 AM, James Lord wrote: > Hi Justin, > I have asked this before, but this time I started up from scratch and used > the input files that I know they are fine but again I am getting this > error, Would you please tell me what is wrong in my topology files and > where about in .top files the bond length are defined? > > > https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing > > Cheers > James > > On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul wrote: > >> >> >> On 5/16/15 11:35 PM, James Lord wrote: >> >>> Hi Justin >>> Thanks for this. Can you tell me which step(s) this bond length is >>> defined >>> What should I do (redo) to resolve this issue? >>> >> >> The bonds are defined in the topology. The DD algorithm reads what's in >> the coordinate file and builds cells based on the geometry it finds there. >> >> Without a full description of what's in your system, what steps you've >> taken to prepare it (full commands, in order), there's little I can suggest >> because it would all be guesswork. >> >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> == >> -- >> 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.
Re: [gmx-users] energy minimization error
On 6/26/15 7:19 PM, James Lord wrote: Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the bond length are defined? https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing There's nothing I can do with a topology that's a series of #include statements. Please also remind me what this is all about so I don't have to go digging through the archives for something from a month ago. Lots of things have happened since then :) -Justin Cheers James On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul wrote: On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based on the geometry it finds there. Without a full description of what's in your system, what steps you've taken to prepare it (full commands, in order), there's little I can suggest because it would all be guesswork. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] energy minimization error
Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the bond length are defined? https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing Cheers James On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul wrote: > > > On 5/16/15 11:35 PM, James Lord wrote: > >> Hi Justin >> Thanks for this. Can you tell me which step(s) this bond length is >> defined >> What should I do (redo) to resolve this issue? >> > > The bonds are defined in the topology. The DD algorithm reads what's in > the coordinate file and builds cells based on the geometry it finds there. > > Without a full description of what's in your system, what steps you've > taken to prepare it (full commands, in order), there's little I can suggest > because it would all be guesswork. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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.
Re: [gmx-users] energy minimization error
On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based on the geometry it finds there. Without a full description of what's in your system, what steps you've taken to prepare it (full commands, in order), there's little I can suggest because it would all be guesswork. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] energy minimization error
Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? Cheers James On Sun, May 17, 2015 at 9:02 AM, Justin Lemkul wrote: > > > On 5/16/15 6:27 AM, James Lord wrote: > >> Dear gmx users, >> I am getting this error, Can anyone help me to get around this? >> Cheers >> James >> >> >> Program mdrun, VERSION 4.6.3 >> Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792 >> >> Fatal error: >> There is no domain decomposition for 8 nodes that is compatible with the >> given box and a minimum cell size of 6.93203 nm >> Change the number of nodes or mdrun option -rdd >> Look in the log file for details on the domain decomposition >> >> >> >> Log file opened on Sat May 16 22:15:44 2015 >> Host: james-E530 pid: 22300 nodeid: 0 nnodes: 1 >> Gromacs version:VERSION 4.6.3 >> Precision: single >> Memory model: 64 bit >> MPI library:thread_mpi >> OpenMP support: enabled >> GPU support:disabled >> invsqrt routine:gmx_software_invsqrt(x) >> CPU acceleration: AVX_256 >> FFT library:fftw-3.3.2-sse2 >> Large file support: enabled >> RDTSCP usage: enabled >> Built on: Wed Oct 30 18:28:46 NZDT 2013 >> Built by: james@james-E530 [CMAKE] >> Build OS/arch: Linux 3.11.0-12-generic x86_64 >> Build CPU vendor: GenuineIntel >> Build CPU brand:Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz >> Build CPU family: 6 Model: 58 Stepping: 9 >> Build CPU features: apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr >> nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 >> sse4.2 ssse3 tdt x2apic >> C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.8.1-10ubuntu8) >> 4.8.1 >> C compiler flags: -mavx-Wextra -Wno-missing-field-initializers >> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter >> -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow >> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 >> -DNDEBUG >> >> >> :-) G R O M A C S (-: >> >>Gromacs Runs On Most of All Computer Systems >> >> :-) VERSION 4.6.3 (-: >> >> Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, >> Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, >> Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph >> Junghans, >> Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, >> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, >> Michael Shirts, Alfons Sijbers, Peter Tieleman, >> >> Berk Hess, David van der Spoel, and Erik Lindahl. >> >> Copyright (c) 1991-2000, University of Groningen, The Netherlands. >> Copyright (c) 2001-2012,2013, The GROMACS development team at >> Uppsala University & The Royal Institute of Technology, Sweden. >> check out http://www.gromacs.org for more information. >> >> This program is free software; you can redistribute it and/or >> modify it under the terms of the GNU Lesser General Public License >> as published by the Free Software Foundation; either version 2.1 >> of the License, or (at your option) any later version. >> >> :-) mdrun (-: >> >> >> PLEASE READ AND CITE THE FOLLOWING REFERENCE >> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl >> GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable >> molecular simulation >> J. Chem. Theory Comput. 4 (2008) pp. 435-447 >> --- Thank You --- >> >> >> PLEASE READ AND CITE THE FOLLOWING REFERENCE >> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. >> C. >> Berendsen >> GROMACS: Fast, Flexible and Free >> J. Comp. Chem. 26 (2005) pp. 1701-1719 >> --- Thank You --- >> >> >> PLEASE READ AND CITE THE FOLLOWING REFERENCE >> E. Lindahl and B. Hess and D. van der Spoel >> GROMACS 3.0: A package for molecular simulation and trajectory analysis >> J. Mol. Mod. 7 (2001) pp. 306-317 >> --- Thank You --- >> >> >> PLEASE READ AND CITE THE FOLLOWING REFERENCE >> H. J. C. Berendsen, D. van der Spoel and R. van Drunen >> GROMACS: A message-passing parallel molecular dynamics implementation >> Comp. Phys. Comm. 91 (1995) pp. 43-56 >> --- Thank You --- >> >> Input Parameters: >> integrator = steep >> nsteps = 5 >> init-step= 0 >> cutoff-scheme= Group >> ns_type = Grid >> nstlist = 5 >> ndelta = 2 >> nstcomm = 100 >> comm-mode= Linear >>
Re: [gmx-users] energy minimization error
On 5/16/15 6:27 AM, James Lord wrote: Dear gmx users, I am getting this error, Can anyone help me to get around this? Cheers James Program mdrun, VERSION 4.6.3 Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792 Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.93203 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition Log file opened on Sat May 16 22:15:44 2015 Host: james-E530 pid: 22300 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6.3 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Wed Oct 30 18:28:46 NZDT 2013 Built by: james@james-E530 [CMAKE] Build OS/arch: Linux 3.11.0-12-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1 C compiler flags: -mavx-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG :-) G R O M A C S (-: Gromacs Runs On Most of All Computer Systems :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) mdrun (-: PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 --- Thank You --- Input Parameters: integrator = steep nsteps = 5 init-step= 0 cutoff-scheme= Group ns_type = Grid nstlist = 5 ndelta = 2 nstcomm = 100 comm-mode= Linear nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy= 100 nstenergy= 1000 nstxtcout= 0 init-t = 0 delta-t = 0.001 xtcprec = 1000 fourierspacing = 0.12 nkx = 56 nky = 56 nkz = 144 pme-order= 4 ewald-rtol = 1e-05 ewald-geometry = 0 epsilon-surface
[gmx-users] energy minimization error
Dear gmx users, I am getting this error, Can anyone help me to get around this? Cheers James Program mdrun, VERSION 4.6.3 Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792 Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.93203 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition Log file opened on Sat May 16 22:15:44 2015 Host: james-E530 pid: 22300 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6.3 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Wed Oct 30 18:28:46 NZDT 2013 Built by: james@james-E530 [CMAKE] Build OS/arch: Linux 3.11.0-12-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1 C compiler flags: -mavx-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG :-) G R O M A C S (-: Gromacs Runs On Most of All Computer Systems :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) mdrun (-: PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 --- Thank You --- Input Parameters: integrator = steep nsteps = 5 init-step= 0 cutoff-scheme= Group ns_type = Grid nstlist = 5 ndelta = 2 nstcomm = 100 comm-mode= Linear nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy= 100 nstenergy= 1000 nstxtcout= 0 init-t = 0 delta-t = 0.001 xtcprec = 1000 fourierspacing = 0.12 nkx = 56 nky = 56 nkz = 144 pme-order= 4 ewald-rtol = 1e-05 ewald-geometry = 0 epsilon-surface = 0 optimize-fft = FALSE ePBC = xyz bPeriodicMols
Re: [gmx-users] Energy minimization error for electroporation simulation of DPPC membrane
On 4/28/15 8:14 AM, Abhijit Jassem wrote: Hi all, I am a beginner to GROMACS and MD simulations in general. I’m trying to model electroporation in a DPPC membrane but I am having issues with the energy minimization step. I am basing my approach on the one followed in Dr. Justin Lemkul’s KALP-15 in DPPC Tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html) but without the steps that use the KALP peptide. After I solvate my membrane, I am trying to run energy minimization, but my steps are moving much slower than normal and I get the error "Water molecule starting at atom 109448 can not be settled. Check for bad contacts and/or reduce the Well, what's going on around atom 109448? timestep if appropriate.” When I looked this error up, I found that this suggested that I had a bad starting structure, possibly with atoms overlapping. Based on this, I assume this error originates when I solvate my membrane. I am currently using the spc216.gro model. Is this an issue with my water model or am I doing something else wrong? There are plenty of potential problems, unfortunately not enough information to go on. Simply using SPC isn't a problem, but something either in the configuration or the force field is an issue. Rather than building a large system (you have over 100,000 atoms), do something small, like the pre-built DPPC bilayer that the tutorial uses. That's a sanity check. If that minimizes and equilibrates well, that means the force field is fine and something is wrong with the way you built your larger system. If you want help with that, you have to tell us exactly what you're doing (exact command sequence). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Energy minimization error for electroporation simulation of DPPC membrane
Hi all, I am a beginner to GROMACS and MD simulations in general. I’m trying to model electroporation in a DPPC membrane but I am having issues with the energy minimization step. I am basing my approach on the one followed in Dr. Justin Lemkul’s KALP-15 in DPPC Tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html) but without the steps that use the KALP peptide. After I solvate my membrane, I am trying to run energy minimization, but my steps are moving much slower than normal and I get the error "Water molecule starting at atom 109448 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate.” When I looked this error up, I found that this suggested that I had a bad starting structure, possibly with atoms overlapping. Based on this, I assume this error originates when I solvate my membrane. I am currently using the spc216.gro model. Is this an issue with my water model or am I doing something else wrong? Thank you all very much for the help! -- Abhijit Jassem School of Nuclear Engineering Purdue University abhijitjas...@gmail.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.