Force Fields not implemented: Difference between revisions

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New page: There are two options if you want to check other force fields which are not implemented in Gaussian09; Option1: You can do one-dimensional potential energy surface scans over a reaction...
 
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go back to [[Main Page]], [[Computational Resources]], [[Chemistry & More]], [[Computational Codes]], [[GAUSSIAN]], [[G09]], [[ONIOM tips]]




There are two options if you want to check other force fields which are not implemented in Gaussian09;
There are two options if you want to check other force fields which are not implemented in Gaussian09;


Option1: You can do one-dimensional potential energy surface scans over a reaction coordinate, where the constrained structure optimisations at the potential energy surface can be performed with ONIOM(DFT:UFF), ONIOM(DFT:DREIDING) or ONIOM (DFT:AMBER), where the iop(1/33=2) option helps to obtain QM and MM parts of the molecule. Then you can do MM optimisations on the QM and MM parts of the molecule separately with MACROMODEL or TINKER, where they have various force filed parameters.   
'''Option1:''' You can do one-dimensional potential energy surface scans over a reaction coordinate, where the constrained structure optimisations at the potential energy surface can be performed with ONIOM(DFT:UFF), ONIOM(DFT:DREIDING) or ONIOM (DFT:AMBER), where the iop(1/33=2) option helps to obtain QM and MM parts of the molecule. Then you can do MM optimisations on the QM and MM parts of the molecule separately with MACROMODEL or TINKER, where they have various force filed parameters.   


Option2: ´External´ keyword.
'''Option2:''' ´External´ keyword.


There are two examples in the G09 test suite which make use of the ´External´ keyword.  
There are two examples in the G09 test suite which make use of the ´External´ keyword.  
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In both cases you could use ´External´ keyword in the input file.
In both cases you could use ´External´ keyword in the input file.


Eg:-
Eg:-
ONIOM(B3LYP/6-31G(d):AM1:External="Script_name") Opt
ONIOM(B3LYP/6-31G(d):AM1:External="Script_name") Opt


How to use external MM program:
'''How to use external MM program:'''


This is not fully implemented in G09. The Gau_External script in the G09 home is an example where we use Gaussian as an external program, specifically 'Gau_External' script helps to run MOPAC as external procedure for ONIOM. You would need to make a copy of this script and modify it to create an input file for other MM programes (Eg. TINKER), and run the MM program with this input, and then use the output from the MM program to generate result files suitable for processing by Gaussian.
This is not fully implemented in G09. The Gau_External script in the G09 home is an example where we use Gaussian as an external program, specifically 'Gau_External' script helps to run MOPAC as external procedure for ONIOM. You would need to make a copy of this script and modify it to create an input file for other MM programes (Eg. TINKER), and run the MM program with this input, and then use the output from the MM program to generate result files suitable for processing by Gaussian.

Latest revision as of 12:01, 17 May 2011

go back to Main Page, Computational Resources, Chemistry & More, Computational Codes, GAUSSIAN, G09, ONIOM tips


There are two options if you want to check other force fields which are not implemented in Gaussian09;

Option1: You can do one-dimensional potential energy surface scans over a reaction coordinate, where the constrained structure optimisations at the potential energy surface can be performed with ONIOM(DFT:UFF), ONIOM(DFT:DREIDING) or ONIOM (DFT:AMBER), where the iop(1/33=2) option helps to obtain QM and MM parts of the molecule. Then you can do MM optimisations on the QM and MM parts of the molecule separately with MACROMODEL or TINKER, where they have various force filed parameters.

Option2: ´External´ keyword.

There are two examples in the G09 test suite which make use of the ´External´ keyword.

(1) Test726 uses a shell script to run g09 as an external process with UFF. The script ´extuffex´ is stored in the g09/bsd directory.

(2) Test769 uses a perl script, mygau, which is stored in the g09/bsd subdirectory. Note that you will likely need to edit mygau to change the path to perl, rather than /usr/local/bin, because most machines store it in /usr/bin.

In both cases you could use ´External´ keyword in the input file.

Eg:-
ONIOM(B3LYP/6-31G(d):AM1:External="Script_name") Opt

How to use external MM program:

This is not fully implemented in G09. The Gau_External script in the G09 home is an example where we use Gaussian as an external program, specifically 'Gau_External' script helps to run MOPAC as external procedure for ONIOM. You would need to make a copy of this script and modify it to create an input file for other MM programes (Eg. TINKER), and run the MM program with this input, and then use the output from the MM program to generate result files suitable for processing by Gaussian.