Yammp Shell: Modify Non-Bonds
Introduction
Simple Commands
Modify the Molecular Environment
Modify the Linesearch Methods for Energy Minimization
Modify the Energy Minimization Methods
Modify the Molecular Dynamics Methods
Modify the Monte Carlo Methods
Modify the Non-Bond Terms During a Simulation
modify non_bonds
   [elec_|vdw_| ]trim_type which  # 1
      [elec_|vdw_| ]trim_on on       # 2
      [elec_|vdw_| ]trim_off off     # 3
   #
      [elec_|vdw_| ]cut_off cut      # 4
   #
      dielectric diel                # 5
      scale scale                    # 6
      power pow                      # 7
   #
   vlatscale vlat                 # 8
   end

Modify the non-bond interactions on the fly. The first four keywords each appear in three variations, prefixed with "elec_", "vdw_" or nothing; the variants affect only the electrostatics function, only the van der Waals function or both respectively. For example elec_trim_on sets the value on for the electrostatics function only while vdw_trim_on sets the value on for the van der Waals function only and the plain trim_on sets the value on for both the electrostatics and van der Waals functions.

(1,2,3) The value of which determines the type of trimming to be done on the electrostatics and/or van der Waals functions. If none (the preset value) then the functions are not altered, i.e., not trimmed. If shift the value of the Shifting function will be multiplied to the original function and if switch the Switching function will be applied instead. The Shifting function has a value of 1 at the origin and it decays to a value of zero at a distance off (preset value 12.0Å) The value of this function is multiplied on the original function (usually the electrostatic function) and at distances greater than off the value of the original function is taken as zero. The Switching function is multiplied on the original function (usually van der Waals) when the distance is between on (preset value 11.0Å) and off; at on the multiplicant is 1 and this decays until at the distance off where the multiplicant is zero. After the distance off the value of the original function is taken to be zero. The electrostatics and van der Waals functions decay very slowly to zero only at inifinite distance. The trimming function accelerates the decay to zero at a finite distance.

(4) When non-bond functions (such as electrostatics and van der Waals) are used a list of non-bond pairs is maintained and updated periodically. The list contains pairs of atoms within the distance cut (preset value 13.0Å) and interactions are calculated only if a pair is in the list. Therefore the magnitudes of distances must follow the rule: on < off < cut.

(5) The dielectric constant is set to the value diel (for example 1 for vacuum, 2-4 for organic media and 80 for water). (6) When the inclusion list version of the electrostatics function (ele+, see descriptor file format) is used the dielectric constant can be scaled by setting scale (preset value 0.5). This value is divided into diel to provide the scaled dielectric constant. (7) pow is set to either 1 (preset value) or 2 for the constant dielectric and the distance dependent dielectric models respectively.

(8) The vector lattice term can be scaled by a factor vlat. This is preset to a value of 1.0.

The electrostatics and van der Waals parameters are normally set in the descriptor file. See the ele-, ele+, vdw+, vdw- records. Details of the trimming functions can be found here.


Modify Bond Constraints for Molecular Dynamics
Modify the CONTRA-MD Method
Defining and Invoking Macros
Control Structures
Examples

 


des format
arc format
yammp shell
exam commands
intro
arc
arcedit
arctransform
checkspider
des
elec2vlat

exam
mimesis
mkchainarc
mkchaindes
mkd3c
mkd3d
mkr2cc
mksnac
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xmd3
xmr2
ympf

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