Thank you, Justin, I am still confused about constraints other than position restraints. As mentioned https://www.quora.com/q/gnvbdldrivyzzipw/Use-of-constraints-in-molecular-dynamics
Should I use constraints also for my system to converge better? As I am doing energy minimization in two steps using steep emtol =100 and constraints= all-bonds, which converges in 9116 steps Step Time 9115 9115.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.35583e+03 4.93367e+03 1.88532e+04 2.36071e+02 6.91634e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.12823e+04 3.37615e+05 -6.30626e+03 -2.68202e+06 5.72973e+03 Potential Pres. DC (bar) Pressure (bar) -2.24140e+06 0.00000e+00 -2.56682e+04 Steepest Descents converged to Fmax < 100 in 9116 steps Potential Energy = -2.2414020e+06 Maximum force = 9.0994179e+01 on atom 76219 Norm of force = 3.3411843e+00 But the second minimization which I am doing in using steep integrator and emtol= 10 and constraints=none shows that:- Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 10 (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) Steepest Descents converged to machine precision in 315 steps, but did not reach the requested Fmax < 10. Potential Energy = -2.2420480e+06 Maximum force = 2.9302316e+02 on atom 4379 Norm of force = 3.5330992e+00 Finished mdrun on rank 0 Sun Feb 16 14:28:08 2020 How should I set the minimization energy of my system as it crashes after some steps of nvt equilibration? Thanks Sadaf Rani Ph.D. visiting student Lancaster university Uk -- 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.