@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 gmx-users-requ...@gromacs.org.
