# Gaussian contact potentials

## Bringing freedom of creativity to the SMOG modeller!

### Download

A tarball is available here. The extension is added to GROMACS v4.5.4. Compile GROMACS as you would any distribution, nothing special is required at compile time. This provides three new non-bonded pair interactions that can be included in the`[ pairs ]`

section of the topology (.top). README.SBM in the root directory has helpful information that is reproduced below. A script that will convert a`[ pairs ]`

section between Lennard-Jones and Gaussians in the all-atom model is available here. The width parameter (sigma) for Calpha models is typically a constant 0.5 Å, regardless of the native distance.Here is an excerpt from a book chapter (Springer book) on the contact potentials in SMOG which will introduce the Gaussians.

### Example topology

```
``````
Excerpt of topology ***************
```

[ pairs ]

;normal LJ 6-12 pairs

4 497 1 6.7105667E-02 1.4373939E-03

5 183 1 8.8991727E-02 1.6851818E-03

5 338 1 1.5051600E-02 1.2052582E-04

5 339 1 1.2527527E-02 8.3485455E-05

6 183 1 5.7529955E-02 7.0429500E-04

; ....

;standalone Gaussian well

1 316 5 0.818992 0.279187 0.0474239

; ...

;Gaussian well with connected a/r^12 repulsive core

;(must be used with [ exclusions ])

1 316 6 0.818992 0.279187 0.0474239 0.59605E-09

; ...

;dual basin Gaussian with connected a/r^12 repulsive core

;(must be used with [ exclusions ])

1 316 7 0.819006 0.279187 0.0474239 0.426216 0.072399 0.59605E-09

; ...

*****************************************************

### Single Gaussian contact potential

From README.SBM:`bare Gaussian potential:`

V_ij = -A exp( - ( r - mu )^2 / ( 2 sigma^2 ) )

selected in the [ pairs ] section;

; i j ftype A mu sigma

with ftype = 5

note that the amplitude of the Gaussian is -A.

This can be used with a separate repulsion term or without it.

----------------------------------------------

combined Gaussian - r^-12 potential:

V_ij = A({ 1 + (1/A)a/(r^12) }{ 1 - exp[ - ( r - mu )^2 / ( 2 sigma^2 ) ] }-1)

= A({ 1 + R/A }{ 1 - G } - 1)

= R - AG - RG

this construction keeps the minimum of V fixed at ( mu, -A )

selected in the [ pairs ] section of the .top file

; i j ftype A mu sigma a

with ftype = 6

note that the amplitude of the Gaussian is -A.

IMPORTANT: the term R (and its derivative) now IS calculated here, the separate repulsion defined in [ atomtypes ] should be removed for each pair using this potential by [ exclusions ] :

; i j

note that the section [ bonds ] must appear before [ exclusions ] (as of 3.3)

### Double well Gaussian contact potential

From README.SBM:`two Gaussians & r^-12 repulsion:`

V_ij = A[ (1+R/A) (1-F) (1-G) - 1]

= R - AF - AG + AFG - FR - GR + FGR

F = exp( - ( r - mu1 )^2 / ( 2 sigma1^2 ) )

G = exp( - ( r - mu2 )^2 / ( 2 sigma2^2 ) )

R = a/(r^12)

selected in the [ pairs ] section;

; i j ftype A mu1 sigma1 mu2 sigma2 a

with ftype = 7

both Gaussians get the common amplitude -A, minima of the resulting function are (mu1,-A) & (mu2,-A) as for the single Gaussian, [ exclusions ] are required

Page created on 4/30/11.

This resource is provided by the Center for Theoretical Biological Physics.

Please direct questions and comments to info@smog-server.org.

Page created and maintained by Jeff Noel and Paul Whitford