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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
>