VMD-L Mailing List

From: Goutham (gouthambs_at_gmail.com)
Date: Wed Apr 01 2009 - 22:43:23 CDT

Hey Peter,
I run the following command on a protein selection to calculate all energy
using PME.

namdenergy -all -sel $prot -pme -extsys minimize.xsc -debug

This gives the following error:
FATAL ERROR: Sorry, pairInteraction not implemented for full electrostatics.

The namd-temp.namd file looks like this:
######################################
structure final.psf
paraTypeCharmm on
parameters
/home1/goutham/lib/vmd-text/plugins/noarch/tcl/readcha
mpar1.0/par_all27_prot_lipid_na.inp
numsteps 1
exclude scaled1-4
outputname namd-temp
temperature 0
COMmotion yes
cutoff 12
dielectric 1.0
extendedSystem minimize.xsc
PME on
PMEGridSizeX 109
PMEGridSizeY 110
PMEGridSizeZ 111

switchdist 10
*pairInteraction on*
pairInteractionGroup1 1
pairInteractionFile namd-temp.pdb
pairInteractionSelf on
coordinates namd-temp.pdb
run 0
#####################################

Here if switch pairInteraction to off in the namd-temp.namd file and run
namd2 on it, then it goes through fine.

I wonder why the -pme flag in namdenergy turns on the pairinteraction to on.
How else can i fix this?

Thanks

Goutham

On Wed, Apr 1, 2009 at 7:43 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:

> Could you be a bit more specific...?
>
> Goutham wrote:
> > I want to use PME method calculate the energy.. When I use the PME flag
> > in namdenergy, i get an error...
> >
> > THanks
> > Goutham
> >
> >
> > On Wed, Apr 1, 2009 at 6:12 PM, Peter Freddolino <petefred_at_ks.uiuc.edu
> > <mailto:petefred_at_ks.uiuc.edu>> wrote:
> >
> >
> >
> > Goutham wrote:
> > > Hey All,
> > >
> > > I am running NAMDEnergy to calculate energy; Here is the command I
> > use:
> > >
> > > namdenergy -all -sel $prot -debug
> > >
> > > This turns the pairInteraction on. Now I am figuring out a way to
> turn
> > > pairinteraction off; otherwise I am not able to do PME..
> >
> > Why do you want to have pairInteractions off, and why would having
> > pairInteractions on not let you use PME?
> >
> > What is it that you want to calculate, exactly?
> > Best,
> > Peter
> >
> > >
> > >
> > > Any suggestions?
> > >
> > > Thanks
> > >
> > > Goutham
> > >
> >
> >
>