geometry question
Just Got Here
1:14:22 PM PST - Thu, Mar 1st 2012
Hello all,

I'm new to NWChem, and trying to run tutorials first. I run AIMD/MM simulation of CCl4 + 64 H2O example listed under NWPW by using Car Parrinello. I visualised my xyz file at the end of the simulation with VMD, and it seemed Cl ions bonded to water molecules. I did the same calculation with different molecule in water, and I got a similar result. The Hydrogen atoms in my molecule seem to be bonded to water molecules. I searched for the geometries, and couldn't find the answer. Is there any keyword that can put in my input file to block the bonding of my molecule and water?

I'll appreciate your help.
Thank you.

geometry units angstrom nocenter noautosym noautoz print xyz
C -0.000283 0.000106 0.000047

Cl -0.868403 1.549888 0.254229

Cl 0.834043 -0.474413 1.517103

Cl -1.175480 -1.275747 -0.460606

Cl 1.209940 0.200235 -1.310743

O^ 0.3226E+01 -0.4419E+01 -0.5952E+01 

H^ 0.3193E+01 -0.4836E+01 -0.5043E+01 

H^ 0.4167E+01 -0.4428E+01 -0.6289E+01

O^ 0.5318E+01 -0.3334E+01 -0.1220E+01

H^ 0.4978E+01 -0.3040E+01 -0.2113E+01

H^ 0.5654E+01 -0.2540E+01 -0.7127E+00

....
end

Clicked A Few Times
5:08:47 PM PDT - Fri, May 4th 2012
I have similar question
Is there anyone who knows the answer? I have similar or the same question with what Lemonseed asked.

Now I'm trying to find the way to keep bonds between atoms within a molecule while doing optimization task.


Now I'm doing QM/MM simulation and trying to optimize a system which contains amino acids in water.

I guess, since amino acids are in aqueous state, some part of them like "COOH" or "NH2" loss or get "H"
By this, the amino acids becomes partially charged and in some cases the whole amino acids becomes ion state.
(Am I right?)


I have pdb files of amino acids that is in partially charged state or ion state.

I placed this pdb file in solvation box by doing prepare task, and runned optimization task.

When the task is over, I checked the output xyz file and found that partially charged region became neutral!

Furthermore, in some cases a hydrogen atom was attached to a part of amino acid where it shouldn't be.
(for example, a hydrogen atom was attached to a carbon atom in benzene ring in amino acid so thatthat carbon atom has 2 hydrogen bond and 2 carbon bond)


I have another question about this. When I run optimization task, the amino aicds moves from their initial position. I don't want to exclude the amino acids in my calculation but just want to fix them in their initial position.
Is there any method to fix certain molecule or atom in their initial position while doing optimization task or other simulation?


If you knows the answer or some hints about the questions, please teach me.

Clicked A Few Times
7:02:56 AM PDT - Tue, May 8th 2012
Well, I think...
I think I found two method to fix the atoms.

I found that I can give constraints about the geometry, with typing...
  set geometry:actlist <integer list_of_center_numbers>
according to the Geometries document page,
"http://nwchemgit.github.io/index.php/Release61:Geometry#Cartesian_coordinate_input"

I found one more method. If I want to fix atom 1 and 8 to 13,
  constraints 

    fix atom 1 8:13 

  end
from "http://nwchemgit.github.io/index.php/Constraints"


Am I right? Here I have another question. what's the difference between above two methods...?!


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