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