Hi all, I am using CHARMM forcefield with tables for Protein SOL interactions for alanine dipeptide. Tables supplied: table.xvg, table_Protein_SOL.xvg, tablep.xvg (Standard tables for 6-12 interactions used) Combination rule changed from '2' to '1' in forcefield.itp file.
In the energy minimization step, using mdrun the following problem is encountered: Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+00 Number of steps = 10000 F-max = 2.98523e+10 on atom 4 F-Norm = 1.32072e+09 step -1: Water molecule starting at atom 1149 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes ;define = -DFLEXIBLE define = -DPOSRES ; Parameters describing what to do, when to stop and what to save integrator = cg ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol nsteps = 10000 ; Maximum number of (minimization) steps to perform nstenergy = 10000 ; Write energies to disk every nstenergy steps energygrps = Protein SOL energygrp_table = Protein SOL ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = User ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) Any suggestions? Pooja -- Quaerendo Invenietis-Seek and you shall discover.
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