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DRF90 (Read 6330 times)
Gerrit-Jan Linker
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DRF90
30.08.09 at 16:06:21
 
DRF90
 
DRF90 is an implementation of the classical-only part of the Direct Reaction Field approach. It uses a polarisable force field.  
 
See also:
DRF: Direct Reaction Field method  
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1216934410
 
Reference:
Marcel Swart's DRF90 information:
http://iqc.udg.es/~marcel/manuals/drf90/index.html
DRF90: a polarizable force field
http://theochem.chem.rug.nl/publications/PDF/ft434.pdf
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« Last Edit: 20.02.10 at 08:25:43 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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DRF90 energy output
Reply #1 - 09.12.09 at 22:28:24
 
DRF90 energy output
 
In the DRF90 output the total DRF energy is split into the following components. Note that this is for a pure classical calculation. Also note that you need to identify sub-systems or fragments in the calculation. The energies are due to forces between these fragments.
 
Dispersion energy
The energy of intermolecular interaction resulting from the interaction between the instantaneous, time-variable dipole of one sub-system and the induced multipole of the second sub-system.  
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1216672162
For the dispersion energy (Udis) the (an)isotropic Slater-Kirkwood expression in DRF90.
 
Electrostatic energy
The interaction between the point charges between the subsystems.
 
Repulsion energy
CHARMM repulsion interaction between atoms in the classical sub-systems.
More info: http://www.cfs.dl.ac.uk/docs/html/part8/node13.html#SECTION000133000000000000000
 

 
The expression used is a function of the number of valence electrons, the polarisability and the distance between the atoms. As the nuclei are only tiny the repulsion is a force where the electron clouds feel eachother. When the atoms are more polarisable the repulsion is reduced.  
Although one can argue that when nuclei are near eachother electrons can 'get out of the way' when the polarisability is high. This effect is not counted as repulsion but as induction energy.
 
Induction energy:  
The induction of an electric moment  in a molecule due to the presence of a permanent electric moment in another molecule.
 
External field (direct)
Efld is the energy related to the interaction of permanent dipoles with an external field (if present).  
 
MECHANICS ENERGY
 
Bonds
 
Angles
 
Dihedrals
 
Improper dihedrals
 
CAVITATION ENERGY
the
Cavitation energy (Ucav) is the energy needed to create a vacuum within a dielectric continuumin which the system is placed, for which the Pierotti’s formulation is used.
 
Wall Force
 
Friedman
 
Pierotti
 
Source:
GAMESS-UK: DRF Output--Analysis of (D)RF Energies  
http://www.cfs.dl.ac.uk/docs/html/part8/node15.html
DRF90: a polarizable force field
http://theochem.chem.rug.nl/publications/PDF/ft434.pdf
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« Last Edit: 15.05.10 at 11:02:51 by Gerrit-Jan Linker »  

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DRF90: External blocks, Groups and Subgroups
Reply #2 - 20.04.10 at 15:18:38
 
DRF90: External blocks, Groups and Subgroups
 
Part of the input of DRF90 is the so called external block. In this block the model system is defined. Every line in the block describes an atom in the system apart from lines indicating the end of a group or a subgroup.
 
On the lines with the atomic data the following fields should be given, separated by a comma.
Atom name, Atom number
Molecule name, Molecule number
Atomic charge
XYZ coordinates (a.u.)
Atomic polarizability (a.u.)
Atomic VdW-radius (a.u.)
 
Example:
P   1, pf6, 1, 1.7178,   0.000000,   0.000000,   0.000000,  1.07883,  3.429
F   2, pf6, 1, -0.4530,   3.055613,   0.000000,   0.000000,  5.98696,  3.414
F   3, pf6, 1, -0.4530,   -3.055613,   0.000000,   0.000000,  5.98696,  3.414
F   4, pf6, 1, -0.4530,   0.000000,   3.055613,   0.000000,  5.98696,  3.414
F   5, pf6, 1, -0.4530,   0.000000,   -3.055613,   0.000000,  5.98696,  3.414
F   6, pf6, 1, -0.4530,   0.000000,   0.000000,   3.055613,  5.98696,  3.414
F   7, pf6, 1, -0.4530,   0.000000,   0.000000,   -3.055613,  5.98696,  3.414

 
The atom name and atom number are used for labeling purposes only.
 
DRF90 is used to calculate the interactions between molecules (groups of molecules or fragments; but molecules is the used term). Point charges and polarisabilities do not act within a molecule. They only interact with other molecules. The way the system of interest is partitioned into molecules is therefore of critical importance.
 
Considering the input lines with atomic data, if the molecule name and number on a particular line is different from the one above a new molecule is started. For example to create a system with 2 interacting PF6 molecules just use 2 different molecule names (e.g. pf6a and pf6b):
P   1, pf6a, 1, 1.7178,   0.000000,   0.000000,   0.000000,  1.07883,  3.429
F   2, pf6a, 1, -0.4530,   3.055613,   0.000000,   0.000000,  5.98696,  3.414
F   3, pf6a, 1, -0.4530,   -3.055613,   0.000000,   0.000000,  5.98696,  3.414
F   4, pf6a, 1, -0.4530,   0.000000,   3.055613,   0.000000,  5.98696,  3.414
F   5, pf6a, 1, -0.4530,   0.000000,   -3.055613,   0.000000,  5.98696,  3.414
F   6, pf6a, 1, -0.4530,   0.000000,   0.000000,   3.055613,  5.98696,  3.414
F   7, pf6a, 1, -0.4530,   0.000000,   0.000000,   -3.055613,  5.98696,  3.414
P   1, pf6b, 1, 1.7178,   0.000000,   0.000000,   0.000000,  1.07883,  3.429
F   2, pf6b, 1, -0.4530,   3.055613,   0.000000,   0.000000,  5.98696,  3.414
F   3, pf6b, 1, -0.4530,   -3.055613,   0.000000,   0.000000,  5.98696,  3.414
F   4, pf6b, 1, -0.4530,   0.000000,   3.055613,   0.000000,  5.98696,  3.414
F   5, pf6b, 1, -0.4530,   0.000000,   -3.055613,   0.000000,  5.98696,  3.414
F   6, pf6b, 1, -0.4530,   0.000000,   0.000000,   3.055613,  5.98696,  3.414
F   7, pf6b, 1, -0.4530,   0.000000,   0.000000,   -3.055613,  5.98696,  3.414

 
These 2 molecules will now interact. P1 in PF6a will interact with P1 in PF6b and also with F2, F3, ... in PF6b. P1 in PF6a will not interact with F2, F3, ... in PF6a as only intermolecular interactions will be computed.
 
If the molecules are defined as above, each charge and polarisability on an atomic site in a particular molecule can interact with another molecule. This quickly gets out of hand as there will be many interacting points. To make calculations cheaper a set of options are available to reduce the number of interactions the program needs to calculate. External points can be grouped in several ways to achieve this. Still all point charges will interact individually but the polarisabilities will be grouped and centered to a single group-polarisability.
In addition, grouping can be used to define separate analysis groups.
 
GROUP
You can group atoms using the GROUP command. The molecule will be closed at that line and a group polarisability will be calculated and placed in the center of the molecule. Grouped atoms in this way will interact with all other molecules in the system because they will form a new molecule. Even when the same molecule name is used in further atomic input lines the use of a GROUP command will create the molecule and all atomic input lines that follow will be placed in another new molecule.
 
To use the GROUP command to define the two PF6 molecules we can use the following input:
P   1, pf6, 1, 1.7178,   0.000000,   0.000000,   0.000000,  1.07883,  3.429
F   2, pf6, 1, -0.4530,   3.055613,   0.000000,   0.000000,  5.98696,  3.414
F   3, pf6, 1, -0.4530,   -3.055613,   0.000000,   0.000000,  5.98696,  3.414
F   4, pf6, 1, -0.4530,   0.000000,   3.055613,   0.000000,  5.98696,  3.414
F   5, pf6, 1, -0.4530,   0.000000,   -3.055613,   0.000000,  5.98696,  3.414
F   6, pf6, 1, -0.4530,   0.000000,   0.000000,   3.055613,  5.98696,  3.414
F   7, pf6, 1, -0.4530,   0.000000,   0.000000,   -3.055613,  5.98696,  3.414
GROUP
P   1, pf6, 1, 1.7178,   0.000000,   0.000000,   0.000000,  1.07883,  3.429
F   2, pf6, 1, -0.4530,   3.055613,   0.000000,   0.000000,  5.98696,  3.414
F   3, pf6, 1, -0.4530,   -3.055613,   0.000000,   0.000000,  5.98696,  3.414
F   4, pf6, 1, -0.4530,   0.000000,   3.055613,   0.000000,  5.98696,  3.414
F   5, pf6, 1, -0.4530,   0.000000,   -3.055613,   0.000000,  5.98696,  3.414
F   6, pf6, 1, -0.4530,   0.000000,   0.000000,   3.055613,  5.98696,  3.414
F   7, pf6, 1, -0.4530,   0.000000,   0.000000,   -3.055613,  5.98696,  3.414

 
 
When doing a MD calculation the group can be specified to be frozen. NOMC is then added to the group: GROUPNOMC. You can also specify NOMC for a group of atoms that do not form a group polarisability. In that case type 5 spaces and then NOMC: _____NOMC.
 
Finally a group can be made part of an analysis group (see below). Just add the analysis group and number to the GROUPNOMC command: GROUPNOMCANAL01 for example. Again here you can group atoms into an analysis group without defining a group polarisability or NOMC for them. Just add 9 spaces to only use the analyis group: _________ANAL02.
 
Any combination of GROUP, NOMC and analsys groups is allowed:  
GROUP____ANAL03
_____NOMCANAL04
__________ANAL05
GROUPNOMC
GROUP____
_____NOMC
 
SUBGR
Subgroups can be used to group the polarisabilities within a single molecule. Then they work similar to ordinary groups. However with subgroups the (sub)groups will not interact as they are part of the same molecule. They will only interact with other molecules and not with molecules of the same name.
 
The same combinations with NOMC and analysis groups can be made.
 
Analysis groups:
When using more than one molecule it may be handy to use analysis groups to group interactions together for analysis purposes. As mentioned before, when making groups of atoms you can optionally place them into analysis groups using the ANALNN keyword where NN should be replaced by a number, e.g. 01.
 
See also:
Marcel Swart's website - drf90 input - external
http://iqc.udg.es/~marcel/eng/
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« Last Edit: 22.04.10 at 14:22:41 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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DRF90: Molecular Dynamics (MD) calculations
Reply #3 - 25.04.10 at 14:20:43
 
DRF90: Molecular Dynamics (MD) calculations
 
To perform a MD calculation with DRF90 you need to set the runflg parameter to 13. An MD block can be used to specify MD specific parameters.  
 
Example input:
CNTRL
 runflg 13
End
IMAGE
 images 1
 rimage 1000
End
MD
 nrsteps 50000
 npunfrq 500
 nprint  500
 OUTFOR "LONGALL NONE"
END
DRF
 IBEM 0
End
 $EXTERNAL
....
 $END

 
MD keywords:
nrsteps n: number of steps
npunfrq n: write to file every n steps
nprint n: print output every n steps
OUTFOR "LONGALL NONE": All data will be written to the sim data file  
 
 
Full input description:
Marcel's DRF documentation - MD:
http://iqc.udg.es/~marcel/eng/drf90/md.html
 
See also:
Molecular Dynamics and Molecular Mechanics
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1228392226
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« Last Edit: 05.06.10 at 22:20:20 by Gerrit-Jan Linker »  

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