[gmx-users] Energy Minimization

Dallas Warren Dallas.Warren at monash.edu
Tue Oct 19 04:11:08 CEST 2010

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.warren at 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-bounces at gromacs.org
[mailto:gmx-users-bounces at 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


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
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
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
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?




Quaerendo Invenietis-Seek and you shall discover.

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