Dear all, I am interested in carrying out a simulation of mPGES-1 protein (PDB id: 4yl3), which is a homotrimer. I am using POPC membrane; equilibrated for 100 ns for this purpose. I was able to align and insert the protein into the membrane using lambada align and inflategro programs, respectively. I was also able to solvate, delete the extra solvent molecules using perl script as described in the KALP15 tutorial. After adding ions, I tried to carry out energy minimization and got this note along with a premature termination at step 14. -------------------------------- "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. Back Off! I just backed up em.gro to ./#em.gro.2# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = 2.4501964e+16 Maximum force = inf on atom 3999 Norm of force = inf -------------- I tried to carry out NVT but received a warning that the potential energy of the system was too high leading to the termination at step 0 ---------- "Fatal error: Step 0: The total potential energy is 9.96795e+14, which is extremely high. The LJ and electrostatic contributions to the energy are 9.96795e+14 and -1.7601e+06, respectively. A very high potential energy can be caused by overlapping interactions in bonded interactions or very large coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology." ------- I tried incorporating "constraints = none" in the em.mdp and redoing the steps, with no luck. Request you to help me resolve this issue. Thank you in advance. Regards, Prasanth. -- 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.