My structure does not contain any ions. Here are the commands that I used: gmx_d pdb2gmx -f nm_*.pdb -o pdb2gmx.pdb -p topol.top -ff amber99sb -water tip3p -ignh
gmx_d editconf -f pdb2gmx.pdb -o editconf.pdb -bt dodecahedron -d 2.5 gmx_d grompp -f cg.mdp -c editconf.pdb -p topol.top -o cg.tpr gmx_d mdrun -deffnm cg -v gmx_d grompp -f bfgs.mdp -t cg.trr -c cg.tpr -p topol.top -o bfgs.tpr -maxwarn 1 gmx_d mdrun -deffnm bfgs -v gmx_d grompp -f nm.mdp -t bfgs.trr -c bfgs.tpr -p topol.top -o nm.tpr The used mdp files: cg.mdp : ; Parameters describing what to do, when to stop and what to save integrator = cg ; Algorithm (cg= Conjugate Gradient minimization) emtol = 0 ; Stop minimization when the maximum force < 10.0 kJ/mol/nm emstep = 0.1 ; Energy step size nsteps = 500000 ; Maximum number of (minimization) steps to perform nstcgsteep = 1000 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions cutoff-scheme = verlet nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 1.0 ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2; Short-range Van der Waals cut-off fourierspacing = 0.12 pme_order = 4 ewald_rtol =1e-09 epsilon_surface = 0 pbc = xyz ; Periodic Boundary Conditions (yes/no) bfgs.mdp: ;mdp for l-bfgs energy minimization define = -DFLEXIBLE constraints = none integrator = l-bfgs ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions cutoff-scheme = verlet nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = Reaction-Field coulomb-modifier = potential-shift ; Treatment of long range electrostatic interactions rcoulomb-switch = 1.0 rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 fourierspacing = 0.12 pme_order = 4 epsilon_surface = 0 ewald_rtol = 1e-9 pbc = xyz ; Periodic Boundary Conditions (yes/no) ; ; Energy minimizing stuff ; emtol = 0.0 emstep = 0.0001 nstcgsteep = 1000 nbfgscorr = 100000 nsteps = 500000 nm.mdp: ; Parameters describing what to do, when to stop and what to save define = -DFLEXIBLE integrator = nm ; Algorithm (normal mode) ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions cutoff-scheme = verlet nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions coulomb-modifier = potential-shift rcoulomb-switch = 1.0 rcoulomb = 1.2 ; Short-range electrostatic cut-off vdwtype = Cut-off vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2; Short-range Van der Waals cut-off fourierspacing = 0.12 pme_order = 4 ewald_rtol =1e-09 epsilon_surface = 0 pbc = xyz ; Periodic Boundary Conditions (yes/no) nsteps = 10000000 From: Smith, Micholas D.<mailto:smit...@ornl.gov> Sent: woensdag 26 februari 2020 14:10 To: Katrien Clerx<mailto:katrien.cl...@student.kuleuven.be>; gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> Subject: Re: [gmx-users] Normal mode analysis Hmmm.... How did you prepare the structure? Also, attachments are stripped from emails to the mailing list, can you please provide your mdp file as plain text in your reply. =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Katrien Clerx <katrien.cl...@student.kuleuven.be> Sent: Wednesday, February 26, 2020 7:52 AM To: gmx-us...@gromacs.org <gmx-us...@gromacs.org> Subject: [EXTERNAL] Re: [gmx-users] Normal mode analysis Yes I used double precision for everything. -Katrien From: Smith, Micholas D.<mailto:smit...@ornl.gov> Sent: woensdag 26 februari 2020 13:39 To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> Subject: Re: [gmx-users] Normal mode analysis Is your build of GROMACS using double precision? NMA typically is performed with double precision, which is not the default gromacs build. -Micholas =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Katrien Clerx <katrien.cl...@student.kuleuven.be> Sent: Wednesday, February 26, 2020 6:31 AM To: gmx-us...@gromacs.org <gmx-us...@gromacs.org> Subject: [EXTERNAL] [gmx-users] Normal mode analysis ?Hello, Currently I am trying to perform a normal mode analysis on my pdb file using Gromacs 2019.3. But during energy minimalisation I can't seem te get my energy low enough. it remains around 10^01-10^00. I used the attached mdp-files. Am I doing something wrong? If so, what am I doing wrong and how can I fix it? Kind regards, Katrien -- 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 * 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.
