TiO2 MD simulation

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Threads 3
Posts 913
11:36:53 AM PDT - Wed, Apr 23rd 2014
(Posted for Saeed that is having trouble using this website)

I am new with both the NWCHEM and molecular dynamics
calculations. I want to simulate TiO2 in the crystalline state. I have
written .par file for Ti and O atoms using literature data which just
include electrostatic and van der Walls parameters and not the bond or
angle parameters. This is because I found that in this ionic system we
do not need to define parameters for bond, angle and etc. I have
written .pdb file using crystalline structure data. I have also
included just the name of my single segment in a .seq file to avoid
automatic inclusion of solvent by the software. The .frg, .sgm, .rst
and .top files were generated using prepare task. Of course, in the
.top and .rst file generation, the bond, angle and etc. definitions
were deleted from .sgm file as it was urged before. Unfortunately when
I want to run a classical molecular dynamics simulation using these
.rst and .top files, I get that "EOF was encountered in the topology
file". Of course, out file just show error that "* 0: Error in
number of solute fractions 0". Hereby I would like to help me to
overcome this problem. All files are attached too. Please let me know
if you need more information.

Saeed

  • Marat Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Threads 2
Posts 43
11:00:05 AM PDT - Tue, Apr 29th 2014
First, I would strongly discourage using NWChem classical MD module to simulate TiO2 crystalline state, especially if you are new to this area. MD module is oriented more towards soft mater systems. You would be much better off looking into plane wave module.

Some of the problems you see likely coming from the fragment file. You should remove all the connectivity fields from there (the ones that have two numbers, e.g. "1 2"). You also should put charges into the fragment file. Your setup also has no information about the periodic nature of the system (e.g. cell size).

Marat

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Posts 16
8:44:57 AM PDT - Wed, Apr 30th 2014
Request
Dear Marat

Thanks a lot. We want to use NWCHEM for classical MD simulation of organic molecules' adsorption from solution on the TiO2 surface. At first we want to be able to use NWCHEM for classical MD simulation. We have removed all the connectivity fields from fragment file. unfortunately we did not find that how add cell size ( Is it necessary, if we do not want to apply periodicity?). Following are used and created files.

Best Regards
Saeed

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Threads 10
Posts 16
8:47:49 AM PDT - Wed, Apr 30th 2014
Request
Dear Marat

Thanks a lot. We want to use NWCHEM for classical MD simulation of organic molecules' adsorption from solution on the TiO2 surface. At first we want to be able to use NWCHEM for classical MD simulation. We have removed all the connectivity fields from fragment file. unfortunately we did not find that how add cell size ( Is it necessary, if we do not want to apply periodicity?). Following are used and created files.

Best Regards
Saeed

pdb file;(TiO2.pdb)

ATOM 1 Ti1 TIO 1 5.164 0.702 -0.905
ATOM 2 O1 TIO 1 7.279 0.372 -0.689
ATOM 3 O2 TIO 1 3.184 0.430 -1.379
ATOM 4 Ti2 TIO 1 1.178 0.699 -0.892
ATOM 5 O3 TIO 1 1.158 2.357 0.210
ATOM 6 O4 TIO 1 1.033 1.887 -2.360
ATOM 7 Ti3 TIO 1 1.117 3.460 -1.242
ATOM 8 O5 TIO 1 5.193 2.406 0.075
ATOM 9 O6 TIO 1 5.325 1.847 -2.470
ATOM 10 Ti4 TIO 1 5.242 3.430 -1.446
ATOM 11 O7 TIO 1 3.149 3.820 -1.537
ATOM 12 O8 TIO 1 7.306 3.822 -1.502
END
fragment file;(TIO.frg)

# This is an automatically generated fragment file
  1. Atom types and connectivity were derived from coordinates
  2. Atomic partial charges are crude estimates
  3. 04/30/14 18:11:29

$TIO
  12    1    1    0
TIO
   1Ti1   Ti        0    0    0    1    1   +2.196000    0.000000

   2 O1   Oi        0    0    0    1    1   -1.098000    0.000000

   3 O2   Oi        0    0    0    1    1   -1.098000    0.000000

   4Ti2   Ti        0    0    0    1    1   +2.196000    0.000000

   5 O3   Oi        0    0    0    1    1   -1.098000    0.000000

   6 O4   Oi        0    0    0    1    1   -1.098000    0.000000

   7Ti3   Ti        0    0    0    1    1   +2.196000    0.000000

   8 O5   Oi        0    0    0    1    1   -1.098000    0.000000

   9 O6   Oi        0    0    0    1    1   -1.098000    0.000000

  10Ti4   Ti        0    0    0    1    1   +2.196000    0.000000

  11 O7   Oi        0    0    0    1    1   -1.098000    0.000000

  12 O8   Oi        0    0    0    1    1   -1.098000    0.000000


segment file; (TIO.sgm)

  1. This is an automatically generated segment file
  2. 04/13/14 13:20:08 
   4.600000

  12   0   0   0    0    0    1    1

   0.000000

   1Ti1       0    0    0    1    1

    Ti        0.000000    0.000000

   2 O1       0    0    0    1    1

    Oi        0.000000    0.000000

   3 O2       0    0    0    1    1

    Oi        0.000000    0.000000

   4Ti2       0    0    0    1    1

    Ti        0.000000    0.000000

   5 O3       0    0    0    1    1

    Oi        0.000000    0.000000

   6 O4       0    0    0    1    1

    Oi        0.000000    0.000000

   7Ti3       0    0    0    1    1

    Ti        0.000000    0.000000

   8 O5       0    0    0    1    1

    Oi        0.000000    0.000000

   9 O6       0    0    0    1    1

    Oi        0.000000    0.000000

  10Ti4       0    0    0    1    1

    Ti        0.000000    0.000000

  11 O7       0    0    0    1    1

    Oi        0.000000    0.000000

  12 O8       0    0    0    1    1

    Oi        0.000000    0.000000

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Threads 10
Posts 16
8:53:42 AM PDT - Wed, Apr 30th 2014
Dear Marat

Thanks a lot. We want to use NWCHEM for classical MD simulation of organic molecules' adsorption from solution on the TiO2 surface. At first we want to be able to use NWCHEM for classical MD simulation. We have removed all the connectivity fields from fragment file. unfortunately we did not find that how add cell size ( Is it necessary, if we do not want to apply periodicity?). Following are used and created files.

Best Regards
Saeed

parameter file; (amber.par)

This is the AMBER96 user defined parameter file for NWChem 3.2 and ARGOS 7.0
Electrostatic 1-4 scaling factor 0.833333
Relative dielectric constant 1.000000
Parameters epsilon R*
Atoms
Ti 47.86700 2.58660E+00 2.20000E-01 1 1111111111 
            22 1.29330E+00 2.20006E-01                              TPS000106 JCP 85, 6720-6727 (1986)
Oi 15.99900 1.41810E+00 3.24500E-01 1 1111111111 
             8 0.70905E+00 3.24500E-01                              TPS000106 JCC 12, 1125-1128 (1991)
Cross
Bonds
Angles
Proper dihedrals
Improper dihedrals
Atom types
Ti 22 0 0 0 0 0 0 0 0 0
                                0  0      0      0      0

                                0  0      0      0      0

Oi 8 0 0 0 0 0 0 0 0 0
                                0  0      0      0      0

                                0  0      0      0      0

End


sequence file; (TiO2.seq)

   1TIO
stop



prepare nw file; (TiO2.nw)

echo
memory noverify heap 1 mb stack 32 mb global 8 mb

start TiO2

prepare
amber

source TiO2.pdb

new_top new_rst

end
task prepare

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Threads 10
Posts 16
8:35:19 AM PDT - Mon, Mar 16th 2015
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