Hi, The problem is often not anything to do with how you used GROMACS. If your input structure has a big pocket of vacuum then atoms will go flying across it and be unhappy. Likewise if a water is too close to a solute atom. Only you can visualize your structures and see such things.
Mark On Sun, 7 Apr 2019 at 12:09, Anjali Patel <[email protected]> wrote: > @Mark Abraham > Thank you for your kind suggestion. I have checked all structures. After > the minimization eater molecules got close. i have changed all possible > input parameters. still got the same error can you please help to point out > where i am wrong? Here, i have used spc.itp and tip3p.itp of gromos53a5.ff. > i attaching my em.mdp file. > em.mdp > ; LINES STARTING WITH ';' ARE COMMENTS > title = Minimization ; Title of run > > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steepest > descent minimization) > emtol = 1400.0 ; Stop minimization when the maximum force > < 10.0 kJ/mol > emstep = 0.001 ; Energy step size > nsteps = 50000 ; Maximum number of (minimization) > steps to perform > ;nbfgscorr = 10 > ;constraints = none > ;lincs-order = 8 > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > nstlist = 1 ; Frequency to update the neighbor > list and long range forces > cutoff-scheme = Verlet > ewald_rtol = 1e-6 > ns_type = grid ; Method to determine neighbor > list (simple, grid) > rlist = 1.2 ; Cut-off for making neighbor > list (short range forces) > coulombtype = PME ; Treatment of long range > electrostatic interactions > rcoulomb = 1.2 ; long range electrostatic > cut-off > vdwtype = PME > vdw-modifier = Potential-shift > rvdw-switch = 1.0 > rvdw = 1.2 ; long range Van der Waals > cut-off > pbc = xyz ; Periodic Boundary Conditions > DispCorr = no > > > > With regards > Anjali Patel > Research Scholar > Department of Physics > The M S University of Baroda, Vadodara-390002 > -- > 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 [email protected]. > -- 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 [email protected].
