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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Look at atom 1149, exactly as the error message has noted.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Is it, or any of it’s neighbours, not quite where it “should”
be?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Monash Institute of Pharmaceutical Sciences</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Sai Pooja<br>
<b>Sent:</b> Tuesday, 19 October 2010 7:26 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] Energy Minimization<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Hi all,<o:p></o:p></p>
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<p class=MsoNormal> <o:p></o:p></p>
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<p class=MsoNormal>I am using CHARMM forcefield with tables for Protein SOL
interactions for alanine dipeptide. <o:p></o:p></p>
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<p class=MsoNormal>Tables supplied: table.xvg, table_Protein_SOL.xvg,
tablep.xvg (Standard tables for 6-12 interactions used)<o:p></o:p></p>
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<p class=MsoNormal>Combination rule changed from '2' to '1' in forcefield.itp
file.<o:p></o:p></p>
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<p class=MsoNormal> <o:p></o:p></p>
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<p class=MsoNormal>In the energy minimization step, using mdrun the
following problem is encountered:<o:p></o:p></p>
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<p class=MsoNormal> <o:p></o:p></p>
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<p class=MsoNormal>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<o:p></o:p></p>
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<div>
<p class=MsoNormal><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<o:p></o:p></p>
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<div>
<p class=MsoNormal>; The following line tell the program the standard locations
where to find certain files<br>
cpp =
/lib/cpp ; Preprocessor<o:p></o:p></p>
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<div>
<p class=MsoNormal>; Define can be used to control processes<br>
;define = -DFLEXIBLE<br>
define = -DPOSRES<o:p></o:p></p>
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<p class=MsoNormal>; 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<o:p></o:p></p>
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<p class=MsoNormal>; 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>
<br clear=all>
<o:p></o:p></p>
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<p class=MsoNormal> <o:p></o:p></p>
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<p class=MsoNormal>Any suggestions?<o:p></o:p></p>
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<div>
<p class=MsoNormal> <o:p></o:p></p>
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<div>
<p class=MsoNormal>Pooja<o:p></o:p></p>
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<div>
<p class=MsoNormal> <o:p></o:p></p>
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<p class=MsoNormal><br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<o:p></o:p></p>
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