VMD-L Mailing List

From: Goutham (gouthambs_at_gmail.com)
Date: Thu Apr 02 2009 - 11:21:27 CDT

Hey Peter,
Thanks. The error goes away with the new executable.

Best
Goutham

On Wed, Apr 1, 2009 at 8:49 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:

> 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
> > > >
> > >
> > >
> >
> >
>