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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