Re: Potential of mean force calculation using colvars in NADM 2.9 package

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu May 16 2013 - 08:19:57 CDT

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
>
>

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:12 CST