VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Apr 01 2009 - 22:49:26 CDT

What version of namd are you using? This should have been fixed awhile
ago... I think anything more recent than 2.6b2 should work.
Peter

Goutham wrote:
> 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
> <mailto: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>
> > <mailto: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
> > >
> >
> >
>
>