Thank you. On Jul 28, 2017 1:56 AM, "Lachele Foley" <[log in to unmask]> wrote: > GLYCAM is like AMBER. It uses the same functional form and modeling > procedures. It is primarily validated using AMBER software. > > > 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) > > If not what weighing factors can be used to define the weightage of non > bonded interactions between bonded atoms. > > As with AMBER, interactions between 1-2 and 1-3 bonded atoms are defined > in such a way that LJ and Coulombic interactions are not used - that is, > those terms are implicitly set to zero by not being defined. The > 'weighting factor' is not relevant: there is nothing to weight. > > I was merely bothered by the mathematical implications of using a zero as > a weighting factor vis-a-vis AMBER because AMBER defines the factors as the > inverse, e.g., 2.0 (=1.0/0.5) for LJ and 1.2 =(1.0/0.8333) for > electrostatic. Therefore, the AMBER equivalents would be 1.0/0.0=infinity, > which is probably not what you had in mind. > > > 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. > > Zero is ok there. I'm still not sure it makes 'sense'. > > 1-4 interactions for GLYCAM get weights of 1.0 for both Coulombic and LJ. > That is, EE and LJ terms are defined and used for 1-4 interactions, and > they are not scaled (the 'weighting factor' is 1.0). > > > On Thu, Jul 27, 2017 at 11:13 PM, Naveen Kumar Vasudevan < > [log in to unmask]> wrote: > >> 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 <(647)%20629-1562> >> =========================================================== >> >> >> >> *From: *Lachele Foley <[log in to unmask]> >> *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 >> >> >> > > > > -- > :-) Lachele > Lachele Foley > CCRC/UGA > Athens, GA USA >