From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri May 17 2013 - 09:21:24 CDT
Hi Yongil,
Indeed, the behavior you see is due to a problem in NAMD version 2.9. I apologize for that, the issue was fixed in CVS a while ago, but that will only be officially released in NAMD 2.10. In the meantime, you can download and use the "nightly build" version of NAMD, which has the fix.
Best,
Jerome
----- Original Message -----
>
> I send the trajectories.
>
>
> 2.8multicore.namd.result.colvars.traj
>
> 2.9multicore.namd.result.colvars.traj
>
>
>
>
> 2013/5/17 Jérôme Hénin < jerome.henin_at_ibpc.fr >
>
>
> Hey,
>
> Can you send me the trajectories, please? I mean the .colvars.traj
> files.
>
>
>
> Thanks,
> Jerome
>
>
> ----- Original Message -----
> >
> > Dear jerome,
> >
> >
> > I send the files that is related NAMD.
> >
> >
> > clarification of directories ;
> > mini - result coordinate, psf and cfg files.
> > colvars2.8multicore - cfg and colvars files used namd 2.8
> > multicore.
> > colvars2.9multicore - cfg and colvars files used namd 2.9
> > multicore.
> >
> >
> >
> > Best regard,
> > Yongil
> >
> >
> >
> > 2013/5/16 Jérôme Hénin < jerome.henin_at_ibpc.fr >
> >
> >
> > Dear Yongil,
> >
> > Can you send me off-list the colvars trajectories for both versions
> > of NAMD?
> >
> > Thanks,
> > Jerome
> >
> >
> >
> >
> > ----- Original Message -----
> > >
> > >
> > >
> > > Dear NAMD users
> > >
> > >
> > >
> > > We perform MD simultaions for potential of mean forece
> > > calculation
> > > using colvars module in NAMD_2.9_Linux-x86_64-multicore package.
> > >
> > > The system is one potassium ion in 2135 waters on NVT esemble (V
> > > =
> > > 40.0 x 40.0 x 40.0 A^3, T = 298.15 K).
> > >
> > > Colvars parameters are below:
> > >
> > >
> > >
> > > colvarsTrajFrequency 2
> > >
> > > colvar {
> > >
> > > name ProjectionXY_ion
> > >
> > > width 2.5
> > >
> > >
> > >
> > > distanceXY {
> > >
> > > main {
> > >
> > > atomNumbersRange { 1-1 }
> > >
> > > }
> > >
> > > ref {
> > >
> > > dummyAtom ( 0.0, 0.0, 0.0 )
> > >
> > > }
> > >
> > > axis (0.0, 0.0, 1.0)
> > >
> > > }
> > >
> > > }
> > >
> > >
> > >
> > > colvar {
> > > name ProjectionZ_ion
> > >
> > > width 0.4
> > >
> > > lowerboundary -15.0
> > > upperboundary 15.0
> > >
> > >
> > >
> > > lowerwallconstant 10.0
> > > upperwallconstant 10.0
> > >
> > >
> > >
> > > distanceZ {
> > > main {
> > > atomNumbersRange { 1-1 }
> > > }
> > > ref {
> > > dummyAtom ( 0.0, 0.0, 0.0 )
> > > }
> > > axis (0.0, 0.0, 1.0)
> > > }
> > > }
> > >
> > >
> > >
> > > harmonic {
> > > colvars ProjectionXY_ion
> > > forceConstant 1.0
> > > centers 0.0
> > > }
> > >
> > >
> > >
> > > harmonic {
> > > colvars ProjectionZ_ion
> > > forceConstant 1.0
> > > centers -10.0
> > > targetCenters 10.0
> > > targetNumSteps 100000
> > > targetNumStages 50
> > > }
> > >
> > >
> > >
> > > Later simulations, i calculate potentail of mean forece using
> > > umbrella sampling with WHAM.
> > >
> > > We expect that the free energy is changed little.
> > >
> > > But, The defference of free enegy between the initial window and
> > > final window is 25.336992 to target centers from centers.
> > >
> > > So, I performed the same simulations using namd2.8_64-multicore
> > > with
> > > the same module and parameter sets.
> > >
> > > In this case, the difference of free energy is 0.095781.
> > >
> > >
> > >
> > > Link to the PMF profiles
> > >
> > >
> > >
> > > I'm wondering why there is some differences between NAMD 2.8 and
> > > 2.9?
> > > Do i need to add other options or paramters about this colvars in
> > > 2.9
> > > package?
> > >
> > >
> > >
> > > Yongil Seo
> > >
> > >
> >
> >
>
>
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