Re: pair Interaction Calculation

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Thu Oct 16 2003 - 17:50:47 CDT

Hi users,

Sorry for my last e-mail, just found out the example in section 8 of the
manual.
Please ignore my question

Thanks,
Ioana

On Thu, 16 Oct 2003, Ioana Cozmuta wrote:

> Hi namd users,
>
> I want to use the Pair Interaction Calculation feature in namd 2.5 but I
> seem not to be able to figure out the right way to do it.
>
> I want to get forces on group 1 from interaction with group 2 calculated
> from a dcd trajectory. The manual says to set "run 0" so that NAMD does
> NOT run any dynamics but only prints the energies/forces. However I want
> NAMD to print the energies/forces at every time step existing in the
> trajectory file. The problem is that it's only giving me the output for
> the first step.
> I would appreciate if anyone could help me with this.
> I am using the configuration file below.
>
> Thank you,
> Ioana
>
> ******************************
> # NAMD CONFIGURATION FILE FOR Kz90
>
> # force field params
> exclude scaled1-4
> 1-4scaling 0.8333
> scnb 2.0
> amber on
> parmfile ./pore1Kspcm.prmtop
> coordinates ./EqSPMK90.coor
> temperature 300
> seed 314159
> switching on
> switchdist 17.5
> cutoff 18.5
> pairlistdist 20.0
> margin 0.0
> rigidBonds all
> timestep 2
> nonBondedFreq 2
> fullElectFrequency 4
> stepsPerCycle 20
> fixedAtoms on
> fixedAtomsForces on
> fixedAtomsFile ./fix_pore_1Kfree.pdb
> fixedAtomsCol B
> pairInteraction on
> pairInteractionFile ./pairInt_Kprot.pdb
> pairInteractionCol B
> pairInteractionSelf off
> pairInteractionGroup1 3
> pairInteractionGroup2 2
> outputname results
> run 0
>
>

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