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...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