From NWChem
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Just Got Here
Threads 2
Posts 4
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| 10:40:26 PM PDT - Mon, Sep 2nd 2013 |
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I finally tried to define two different MM carbon atoms in my PSPW QM/MM, aka the two different carbons of ethanol, which is my solvent. They have different partial charges and Lennard Jones parameters, hence they need different MM pseudopotentials created, different entries into libraryps/pspw_default/, and the LJ parameters need to be defined for their atom type in the input file.
Let me give you some background - initially I just had one type of MM carbon atom, so I created the C^ file in libraryps/pspw_default/. At the time all of the carbons in my MM section were just listed C (but then they are made into C^ when the mm tags are applied by my mm_tags command), and a C^ psp was created with the mm_psp C^ command after which it was compiled into C^.vpp. C^ LJ parameters were also defined in the input file and interactions between C^ and the rest of the atom types in the simulation were printed in the output file.
When trying to switch to two different types of MM C atoms, I labeled all of the Cs in my MM section C1 and C2, respectively. I created entries C1^ and C2^ in the library, called mm_psp C1^ and mm_psp C2^, and defined their LJ parameters in the input file. I also deleted C^ psps and vpps from my directory, as well as deleting the C^ entry in the library, since I figured they were not necessary. However, this failed to run because it could not find the C^ library entry - despite the fact that I didn't have a C^ type atom in my entire MM section nor any other reference to such an atom type throughout my input.
So then I put a C^ entry back into the library, setting its parameters to those of C1. The program then successfully ran, but while it did make C1^ and C2^ psps, as it was forced to with mm_psp C1^ and mm_psp C2^, it didn't compile them into vpps. Additionally, it did not use the C1^ or C2^ LJ parameters and did not list interactions between C1^ and C2^ mm atoms and the rest of the atoms in the system. However, it did report C^ LJ parameters (which were automatically set to a default of 0.0 and 0.0 because I did not list them in the input file), and it did list C^ interactions with the rest of the atoms.
End result is it clearly is not using C1^ and C2^ and I've no idea how to make it do so. Any help would be greatly appreciated!
Sam
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Just Got Here
Threads 2
Posts 4
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| 2:23:52 PM PDT - Thu, Sep 5th 2013 |
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As per an e-mail response by Eric Bylaska:
You just add a 1 or 2 character label after the "^"
Here's an example where I specified two different oxygens. In addition to the LJ parameters, you'll also need include an mm_psp command to generate a psp potential for the "O^1" MM atom.
Eric
title "CCl4 + 3water64"
start CCl4-water3
scratch_dir ./perm
permanent_dir ./perm
charge 0
geometry units angstrom nocenter noautosym noautoz print xyz
C 0.7929E-02 -0.2760E-02 0.1903E-02
Cl -0.8602E+00 0.1547E+01 0.2561E+00
Cl 0.8423E+00 -0.4773E+00 0.1519E+01
Cl -0.1167E+01 -0.1279E+01 -0.4588E+00
Cl 0.1218E+01 0.1974E+00 -0.1309E+01
O^1 0.3253E+01 -0.4435E+01 -0.5947E+01 -0.2397E-04 -0.1467E-03 -0.7805E-05
H^ 0.3215E+01 -0.4846E+01 -0.5036E+01 -0.6720E-04 -0.1204E-04 0.7077E-04
H^ 0.4195E+01 -0.4458E+01 -0.6283E+01 0.4576E-04 -0.1418E-03 0.8799E-04
O^ 0.5344E+01 -0.3346E+01 -0.1214E+01 -0.3312E-04 -0.8827E-04 0.1682E-04
H^ 0.5001E+01 -0.3063E+01 -0.2109E+01 0.2729E-03 -0.1219E-03 -0.1323E-03
H^ 0.5678E+01 -0.2546E+01 -0.7162E+00 -0.8406E-04 -0.5326E-04 -0.4349E-05
O^ 0.3991E+01 -0.1538E+01 0.1664E+01 -0.3050E-04 -0.1426E-03 -0.1117E-04
H^ 0.4084E+01 -0.2240E+01 0.2370E+01 -0.7053E-04 -0.1202E-03 0.6620E-04
H^ 0.4880E+01 -0.1110E+01 0.1501E+01 0.8933E-05 -0.1389E-03 0.5445E-04
end
set nwpw:cif_filename ccl4water
NWPW
QMMM
mm_psp O^1 -0.8476 4 0.70
lj_ion_parameters C 3.41000000d0 0.10000000d0
lj_ion_parameters Cl 3.45000000d0 0.16d0
lj_ion_parameters O^ 3.16555789d0 0.15539425d0
lj_ion_parameters O^1 3.26555789d0 0.15539425d0
# new input format
fragment spc
size 3
index_start 6:12:3
#shake units angstroms 1 2 3 cyclic 1.0 1.632993125 1.0
bond_spring 1 2 0.467307856 1.889726878
bond_spring 1 3 0.467307856 1.889726878
angle_spring 2 1 3 0.07293966 1.910611932
end
END
END
- Setup conjugate gradient code ****
nwpw
SIMULATION_CELL
#boundary_conditions aperiodic
SC 14.00
ngrid 16 16 16
END
lmbfgs
mapping 2
translation on
np_dimensions 1 2
tolerances 1.0e-11 1.0e-11
end
task pspw energy
task pspw gradient
set geometry:actlist 6:197
nwpw
car-parrinello
#Nose-Hoover 1410.0 300.0 1410.0 300.0 clear
initial_ion_temperature none
time_step 5.00
fake_mass 750.0
loop 2 2
end
end
task pspw car-parrinello
task pspw noit_energy
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Clicked A Few Times
Threads 10
Posts 16
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| 5:20:06 AM PST - Sat, Mar 1st 2014 |
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Dear Sblau
We are a small group starting to play MD with nwchem. Unfortunately we are new with MD. Hereby I would like to have the form of Lennard-Jones equation from which parameter files are written in nwchem. Also, symbols for definition of TiO2 bulck and surface atoms in .par and .frg files. Also, the form of definition of an organic liquid which is adsorbed on the TiO2: number of organic molecules in the PDB and FRG files. I am searching for several weeks in nwchem forum and other places, but I can not find any help except to the QMMM appendix page which is not useful for me.
Best Regards
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