Could someone assist me seeing as i am only a beginner at molecular dynamics
i have generated models using modeller software and selected the best model based on DOPE GA341 and
Prosa now i have performed energy minimisations using gromacs software. I further energy refined the structures using gromacs. The steps were as follows: For in vacuo minimisation Steepest descent 1000 steps and conjugated gradient of 3000 steps. Could you perhaps just check the parameter files (st.mdp and con.mdp) and commands (commands) used to ensure the correct procedures and selections were made in order to ensure my peace of mind. The command files contain outputs I also performed minimisations using periodic boundary conditions adding ions and solvated the system this also were performed using similar conditions as in the in vacuo minimisation. These files are also attached parameter files (em.mdp and con1.mdp) and commands (commands1). Thank you very much i appreciate any and all advice given by you. Best Regards Ruben Cloete South Africa
; Conjugate gradient with morse potential in vacuo ; User Kerrigan (236) ; ; Input file ; cpp = /usr/bin/cpp constraints = none integrator = cg nsteps = 3000 ; ; Energy minimising stuff ; emtol = 100 emstep = 0.01 nstcgsteep = 1000 nstcomm = 1 ns_type = grid morse = yes coulombtype = Shift vdw_type = Shift rlist = 1.0 rcoulomb = 1.2 rvdw = 1.2 rcoulomb_switch = 1.0 rvdw_switch = 1.0 epsilon_r = 6.0 Tcoupl = no Pcoupl = no gen_vel = no
; Steepest Descents in vacuo ; User Kerrigan (236) ; ; Input file ; cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 1000 ; ; Energy minimising stuff ; emtol = 1000.0 emstep = 0.01 nstcomm = 1 ns_type = grid morse = no coulombtype = Shift vdw_type = Shift rlist = 1.0 rcoulomb = 1.2 rvdw = 1.2 rcoulomb_switch = 1.0 rvdw_switch = 1.0 epsilon_r = 6.0 Tcoupl = no Pcoupl = no gen_vel = no
In vacuo energy minimisation pdb2gmx -f cmk.pdb -o cmk.gro -p cmk.top -ignh use Gromos 96.1 (43A2) 1 editconf -bt cubic -f cmk.gro -d 1.0 editconf -f out.gro -o cmk_ctr.gro -center 3.89025 3.89025 3.89025 steepest descents (1000 steps) grompp -f st.mdp -c cmk_ctr.gro -p cmk.top -o cmk_em.tpr mdrun -s cmk_em.tpr -o cmk_em.trr -c cmk_EM_vacuum.pdb -g em.log -e em.edr & Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 1000 writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 5 steps Potential Energy = -4.9777656e+03 Maximum force = 5.3928821e+02 on atom 682 Norm of force = 1.3912250e+02 conjugated gradient (3000 steps) grompp -f con.mdp -c cmk_ctr.gro -p cmk.top -o cmk_em.tpr mdrun -s cmk_em.tpr -o cmk_em.trr -c cmk_EM_vacuum.pdb -g em.log -e em.edr & Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+02 Number of steps = 3000 F-max = 2.80126e+04 on atom 1512 F-Norm = 7.57882e+03 writing lowest energy coordinates. Back Off! I just backed up cmk_EM_vacuum.pdb to ./#cmk_EM_vacuum.pdb.1# Polak-Ribiere Conjugate Gradients converged to Fmax < 100 in 68 steps Potential Energy = -4.9642773e+03 Maximum force = 9.7731384e+01 on atom 1636 Norm of force = 2.3101681e+01
ion wet energy minimisation pdb2gmx -f cmk.pdb -o cmk.gro -p cmk.top -ignh use Gromos 96.1 (43A2) 1 editconf -bt cubic -f cmk.gro -d 1.0 7.78050 7.78050 7.78050 editconf -f out.gro -o cmk_ctr.gro -center 3.89025 3.89025 3.89025 genbox -cp cmk_ctr.gro -cs spc216.gro -o cmk-b4em.gro -p cmk.top Output configuration contains 46207 atoms in 14923 residues Volume : 471.002 (nm^3) Density : 1045.51 (g/l) Number of SOL molecules: 14693 grompp -f em.mdp -c cmk-b4em.gro -p cmk.top -o cmk_em.tpr NOTE 1 [file cmk.top, line 13399]: System has non-zero total charge: -5.999998e+00 genion -s cmk_em.tpr -o cmk_ion.gro -pname NA+ -np 6 -g cmk_ion.log Select a group: 12 Steepest descents (1000 steps) I must run it again grompp -f em.mdp -c cmk_ion.gro -p cmk.top -o cmk_em.tpr mdrun -s cmk_em.tpr -o cmk_em.trr -c cmk_EM_ionwet.pdb -g em.log -e em.edr & Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 1000 ruben@rubennb:~/Desktop/EM_latest/Rv1712_ionwet$ ps PID TTY TIME CMD 1844 pts/0 00:00:00 bash 2506 pts/0 00:04:03 mdrun 2531 pts/0 00:00:00 ps ruben@rubennb:~/Desktop/EM_latest/Rv1712_ionwet$ writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 696 steps Potential Energy = -7.9864450e+05 Maximum force = 9.1239026e+02 on atom 109 Norm of force = 2.3338303e+01 Conjugated gradient (3000 steps) I must run it again grompp -f con.mdp -c cmk_ion.gro -p cmk.top -o cmk_em.tpr mdrun -s cmk_em.tpr -o cmk_em.trr -c cmk_EM_ionwet.pdb -g em.log -e em.edr & Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+03 Number of steps = 3000 F-max = 7.62182e+05 on atom 1815 F-Norm = 5.25147e+03 writing lowest energy coordinates. Back Off! I just backed up cmk_EM_ionwet.pdb to ./#cmk_EM_ionwet.pdb.1# Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 32 steps Potential Energy = -7.4641175e+05 Maximum force = 8.9718903e+02 on atom 1817 Norm of force = 7.3749023e+01
title = Rv1712 cpp = /usr/bin/cpp ; location of cpp on SGI define = -DFLEXIBLE constraints = none integrator = cg dt = 0.002 ; ps ! nsteps = 3000 nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System ; Which energy group(s) to write to disk nstlist = 10 ; do a steep every 10 steps of cg coulombtype = PME ; Use particle-mesh ewald ns_type = grid rlist = 0.9 rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes pbc = xyz ; Periodic Boundary Conditions (yes/no) ; ; energy minimising stuff ; emtol = 1000.0 emstep = 0.01 ; used with conjugate gradient
title = Rv1712 cpp = /usr/bin/cpp ; location of cpp on SGI define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 1000 nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System ; Which energy group(s) to write to disk nstlist = 10 ; do a steep every 10 steps of cg coulombtype = PME ; Use particle-mesh ewald ns_type = grid rlist = 0.9 rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes pbc = xyz ; Periodic Boundary Conditions (yes/no) ; ; energy minimising stuff ; emtol = 1000.0 emstep = 0.01 ; used with steep
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