Re: pair interaction energy for 2 water molecules

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 29 2010 - 04:56:45 CST

On Mon, Nov 29, 2010 at 5:00 AM, divya nayar <divya.alchemist_at_gmail.com> wrote:
> Hi,
> I want to calculate the pair interaction energy between 2 water molecules in
> a system of 256 waters. My conf file is below.
> I am able to reproduce the van der Waal's component of pair interaction
> energy by manual calculations using LJ potential defined in User's guide. I
> want to ask how should I change my PME parameters to tell NAMD to calculate
> the electrostatic energy between only those two tagged water molecules in a
> system of 256 water molecules because the electrostatic energy  for 2
> molecules that I am getting is not very much different from that of between
> one molecule interacting with all other 255 molecules.

you cannot do what you describe _at all_ with PME enabled
or any other type of ewald sum. you have a component of the
electrostatic interaction that is not pair-wise additive and thus
cannot be attributed to arbitrary pairs of atoms or molecules.

axel.

> Also, is there a way I can check the values tht I am getting for
> electrostatic energy are correct?
> structure          ./../tip4p.psf
> coordinates        ../../tip4p-prod260.coor
>
> set outputname     4tip.tpe
>
> temperature         260
> seed                4010
>
> paraTypeCharmm      on
> #parameters          ../par_all27_prot_lipid.inp
> parameters          ../../tip4p.par
>
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling          1.0
> dielectric              1.0
> cutoff              9.5
> switching           on
> switchdist          7.5
> pairlistdist        11.5
> margin              0.0
> # Integrator Parameters
> timestep            1.0  ;# 2fs/step
> rigidBonds          all  ;# needed for 2fs steps
> nonbondedFreq       1
> fullElectFrequency  2
> stepspercycle       20
> rigidTolerance      0.00001
> rigidIterations     100
> wrapAll             on
> wrapWater           on
>
> waterModel        tip4
> # Periodic Boundary Conditions
> PME                 yes
> PMETolerance        0.000001
> PMEGridSizeX        40
> PMEGridSizeY        40
> PMEGridSizeZ        40
>
>
> # Output
> outputName          $outputname
> outputTiming        500
> extendedSystem      ../../tip4p-prod260.xsc
> pairInteraction     on
> pairInteractionFile  ../pdb/abc.pdb
>
> pairInteractionCol B
> pairInteractionGroup1 1
> pairInteractionGroup2 2
> #############################################################
> ## EXECUTION SCRIPT                                        ##
> #############################################################
> set ts 100
>
> coorfile open dcd   ../8000.dcd
>
> while {! [coorfile read] } {
>    firstTimestep $ts
>    run 0
>    incr ts 100
> }
>
> coorfile close
>
>
>
>
> Please guide me. Thanks in advance
>
> Divya

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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