Thank you, I think I framed my doubt wrongly, as per LAMMPS manual,

 

special_bonds (used keywords – angle and dihedrals) command is used to set weighting coefficients for pairwise energy and force contributions between pairs of atoms that are also permanently bonded to each other, either directly or via one or two intermediate bonds.

 

The rationale for using these weighting factors is that the interaction between a pair of bonded atoms is all (or mostly) specified by the bond, angle, dihedral potentials, and thus the non-bonded Lennard-Jones or Coulombic interaction between the pair of atoms should be excluded (or reduced by a weighting factor)

 

this will be an issue if two dihedrals or angles are not defined consecutively,

 

For example, imagine the 1-4 weighting factor is set to 0.5 and you have a linear molecule with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a dihedral, then the pairwise interaction between atoms 1 and 4 will always be weighted by 0.5, but different force fields use different rules for weighting the pairwise interaction between atoms 2 and 5. If the dihedral keyword is specified as yes, then the pairwise interaction between atoms 2 and 5 will be unaffected (full weighting of 1.0). If the dihedral keyword is specified as no which is the default, then the 2,5 interaction will also be weighted by 0.5

 

But GLYCAM defines all dihedrals and angles properly ( so this shouldn’t pose any issue). My doubts were these,

 

  1. Whether the interactions between pair of bonded atoms are defined by corresponding potentials so that the non-bonded Lennard-Jones or Coulombic interaction between the pair of these bonded atoms can be excluded (or reduced by a weighting factor)

 

  1. If not what weighing factors can be used to define the weightage of non bonded interactions between bonded atoms.

 

  1. 0 for 1-2 and 1-3 makes sense since all interactions would have been included in their potential, but I am concerned about dihedrals or 1-4 interactions, for eg. Incase of CHARMM all weighing factors are 0 which means no need to concern oneself to include any sort of non bonded interactions between bonded atoms, I am confused as to whether GLYCAM can be considered similarly to CHARMM or AMBER.

 

I am trying to understand the procedure better.

 

Thank you

 

Regards

Naveen

 

===========================================================
Naveen Kumar Vasudevan, Graduate student,
The Xi Research Lab,
Dept. of Chemical Engineering, McMaster University,
JHE- 296, 1280 Main St. W., Hamilton, ON L8S 4L7, Canada
Email: [log in to unmask] ; Tel: +1(647) 629-1562
===========================================================

 

From: Lachele Foley
Sent: July 27, 2017 9:47 AM
To: [log in to unmask]
Subject: Re: weighing factor for 1-2,1-3,1-4 interactions - reg. (LAMMPS)

 

...as was pointed out, it is worth saying that there are no electrostatic or non-bonded terms for 1-2 and 1-3 interactions in AMBER.  So, zero would be ok.  But, the terms are zero to start with.

 

 

On Thu, Jul 27, 2017 at 8:31 AM, Lachele Foley <[log in to unmask]> wrote:

I am unfamiliar with the modeling procedures in Lammps.  I am concerned by the use of '0.0' as a weighting factor.  The true default weighting factors are 1.0, 1.0, 0.5 and 1.0, 1.0, 0.8333.  That is, 1-2 and 1-3 interactions are not changed from their entries in the parameter files, and, thus are effectively multiplied by 1.0.  Multiplying by zero would have undesirable effects, but perhaps the Lammps format responds appropriately to such a designation.

 

For GLYCAM parameters, the 1-4 weights should be 1.0 as well.  These are indicated in the parameter file.  To see what I mean, search the file at the following link for the terms SCEE and SCNB: http://glycam.org/docs/forcefield/wp-content/uploads/sites/6/2014/02/GLYCAM_06j.dat 

 

 

On Wed, Jul 26, 2017 at 1:52 PM, Naveen Kumar Vasudevan <[log in to unmask]> wrote:

Hi all,

I am simulating CNC using GLYCAM in Lammps, where I use the special_bonds command to define the weighing factors for  1-2,1-3,1-4 atom's  LJ interaction and Coulombic interactions.

I am using AMBER's weighing factor values of 0.0, 0.0, 0.5 (LJ interactions) and 0.0, 0.0, 0.8333 (Coulombic) for 1-2,1-3,1-4 interactions respectively.

Are these weighing factors fine for GLYCAM as well.

Thank you,

Regards
Naveen



 

--

:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA



 

--

:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA