[gmx-users] steepest descents followed by conjugated gradient
Hi Justin i see lots of papers perform steepest descent followed by conjugated gradients. My question do i use the .gro output file as input to perform conjugated gradient minimization as shown in the commands below? or do i repeat pdb2gmx, editconf and genbox on the trajectory file (protA_em.trr) which i must convert to a .pdb file? nohup mdrun -s protA_em.tpr -o protA_em.trr -c *protA_b4pr.gro* -g em.log -e em.edr & Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 1000 writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 754 steps Potential Energy = -6.8864319e+05 Maximum force = 9.1053461e+02 on atom 499 Norm of force = 2.2879843e+01 Now i run conjugated gradient (500 steps) grompp -f em2.mdp -c *protA_b4pr.gro* -p Rv1712.top -o protA_1em.tpr nohup mdrun -s protA_1em.tpr -o protA_em1.trr -c protA_b4pr_1.gro -g em.log -e em.edr & when i run these i get an error message segmentation fault? which i know is usually a memory problem. Thanks Ruben -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: Fwd: Need some assistence
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) = 1.0e+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) = 1.0e+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: -5.98e+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) = 1.0e+03 Number of steps= 1000 ruben@rubennb:~/Desktop/EM_latest/Rv1712_io
