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Subject: RE: [NWCHEM] QM/MM geometry constraints
Date: Fri, 6 Jul 2007 09:49:02 -0700
Message-ID: <9EA84B4DE79CD74F89F814624913B70503AA180E@EMAIL01.pnl.gov>
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Thread-Topic: [NWCHEM] QM/MM geometry constraints
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References: <59F8E9364A4B184EA893B98611CFC88E01617113@XMAIL.ds.utpa.edu>
From: "Valiev, Marat" <marat.valiev@pnl.gov>
To: "Mark Cunningham" <cunningham@utpa.edu>, <nwchem-users@emsl.pnl.gov>
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Mark,

=20

QM/MM module does not use internal coordinates representation, thus your
errors.

Also aside the potential use, the actual charmm fragment files have
never been tested.

I would recommend using AMBER force field.

=20

Marat Valiev, Ph.D.
Senior Research Scientist
Molecular Sciences Software Group (NWChem)
marat.valiev@pnl.gov



 =20

From: owner-nwchem-users@emsl.pnl.gov
[mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Mark Cunningham
Sent: Thursday, July 05, 2007 1:40 PM
To: nwchem-users@emsl.pnl.gov
Subject: [NWCHEM] QM/MM geometry constraints

=20

I am trying to use NWChem 5.0 to perform QM/MM calculations but my
progress

has been hampered by the fact that none of the examples in the
distribution

actually run.  Additionally, it appears that all of the CHARMM fragment
files are

incorrect.

=20

My problem at the moment is to specify a geometry constraint.  In an all
QM

calculation, I can use zcoord to force an atom-atom distance to be some
value

without having to use an harmonic restraint.  In a QM/MM calculation, I
tried using=20

the same strategy: after task prepare, I specified:

=20

geometry
   zcoord
      bond 77 153 3.5 constant
      torsion 69 71 77 153 178.12 constant
   end
end

This results in the following error:

User specification of redundant internal variables
 --------------------------------------------------

   i   j   k   l     value       name   frz
  --- --- --- --- ------------ -------- ---
   77 153             3.500000 User001    T
   69  71  77 153   178.120000 User002    T


 Scaling coordinates for geometry "geometry" by  1.889725989
 (inverse scale =3D  0.529177249)

  geom_cart_set: too many centers                      0 geometry
  geom_masses_set: too many centers                      0 geometry
  geom_nucexps_set: too many centers                      0 geometry
=20
------------------------------------------------------------------------
 geom_input: geom_nucexps_set failed        0
=20
------------------------------------------------------------------------
=20
------------------------------------------------------------------------
  current input line :
    42: end
=20
------------------------------------------------------------------------

I would appreciate any advice.

=20

Mark A Cunningham

The University of Texas-Pan American

=20


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<div class=3DSection1>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>Mark,<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>QM/MM module does not use internal coordinates =
representation, thus
your errors.<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>Also aside the potential use, the actual charmm fragment =
files have
never been tested.<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>I would recommend using AMBER force =
field.<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;color:blue'>Marat =
Valiev,
Ph.D.<br>
Senior Research Scientist<br>
Molecular Sciences Software Group (NWChem)<br>
marat.valiev@pnl.gov<br>
<br>
</span><span style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;color:blue'>&nbsp;</span><span
style=3D'color:blue'> </span><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p></o:p></span></p>

<div>

<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt =
0in 0in 0in'>

<p class=3DMsoNormal><b><span =
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span>=
</b><span
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
owner-nwchem-users@emsl.pnl.gov [mailto:owner-nwchem-users@emsl.pnl.gov] =
<b>On
Behalf Of </b>Mark Cunningham<br>
<b>Sent:</b> Thursday, July 05, 2007 1:40 PM<br>
<b>To:</b> nwchem-users@emsl.pnl.gov<br>
<b>Subject:</b> [NWCHEM] QM/MM geometry =
constraints<o:p></o:p></span></p>

</div>

</div>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>I am trying to use NWChem 5.0 to perform QM/MM calculations =
but my
progress</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>has
been hampered by the fact that none of the examples in the =
distribution</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>actually
run.&nbsp; Additionally, it appears that all of the CHARMM fragment =
files are</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>incorrect.</s=
pan><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>My
problem at the moment is to specify a geometry constraint.&nbsp; In an =
all QM</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>calculation,
I can use zcoord&nbsp;to force&nbsp;an atom-atom distance to be some =
value</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>without
having to use an harmonic restraint.&nbsp; In&nbsp;a QM/MM calculation, =
I tried
using </span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>the
same strategy: after task prepare, I specified:</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>geometry<br>
&nbsp;&nbsp; zcoord<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; bond 77 153 3.5 constant<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; torsion 69 71 77 153 178.12 constant<br>
&nbsp;&nbsp; end<br>
end</span><o:p></o:p></p>

</div>

<p><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>This results
in the following error:</span><o:p></o:p></p>

<p><span style=3D'font-size:10.0pt;font-family:"Courier New"'>User =
specification
of redundant internal variables<br>
&nbsp;--------------------------------------------------</span><o:p></o:p=
></p>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>&nbsp;&nbsp;
i&nbsp;&nbsp; j&nbsp;&nbsp; k&nbsp;&nbsp; l&nbsp;&nbsp;&nbsp;&nbsp;
value&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; name&nbsp;&nbsp; frz<br>
&nbsp; --- --- --- --- ------------ -------- ---<br>
&nbsp;&nbsp; 77
153&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;
3.500000 User001&nbsp;&nbsp;&nbsp; T<br>
&nbsp;&nbsp; 69&nbsp; 71&nbsp; 77 153&nbsp;&nbsp; 178.120000
User002&nbsp;&nbsp;&nbsp; T</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt'><br>
</span><span style=3D'font-size:10.0pt;font-family:"Courier =
New"'>&nbsp;Scaling
coordinates for geometry &quot;geometry&quot; by&nbsp; 1.889725989<br>
&nbsp;(inverse scale =3D&nbsp; 0.529177249)</span><span =
style=3D'font-size:10.0pt'><o:p></o:p></span></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>&nbsp;
geom_cart_set: too many
centers&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
0 geometry<br>
&nbsp; geom_masses_set: too many
centers&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
0 geometry<br>
&nbsp; geom_nucexps_set: too many
centers&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
0 geometry<br>
&nbsp;-------------------------------------------------------------------=
-----<br>
&nbsp;geom_input: geom_nucexps_set
failed&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br>
&nbsp;-------------------------------------------------------------------=
-----<br>
&nbsp;-------------------------------------------------------------------=
-----<br>
&nbsp; current input line :<br>
&nbsp;&nbsp;&nbsp; 42: end<br>
&nbsp;-------------------------------------------------------------------=
-----</span><span
style=3D'font-size:10.0pt'><o:p></o:p></span></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>I
would appreciate any advice.</span><span =
style=3D'font-size:10.0pt'><o:p></o:p></span></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt'>&nbsp;<o:p></o:p></span></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>Mark
A Cunningham</span><span =
style=3D'font-size:10.0pt'><o:p></o:p></span></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>The
University of Texas-Pan American</span><span =
style=3D'font-size:10.0pt'><o:p></o:p></span></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'>&nbsp;<o:p></o:p></span></p>

</div>

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