Look at atom 1149, exactly as the error message has noted.
Is it, or any of it's neighbours, not quite where it "should" be? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Sai Pooja Sent: Tuesday, 19 October 2010 7:26 AM To: Discussion list for GROMACS users Subject: [gmx-users] Energy Minimization 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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