From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Apr 10 2014 - 12:03:27 CDT
Hello Naresh you should define the same axis for both variables.
Giacomo
On Apr 10, 2014 12:37 PM, "naresh kumar" <naresh.cmds_at_gmail.com> wrote:
> Hi all,
> I am using Collective Variable module in NAMD to get the free
> energy profiles. I have been using the colvars module in NAMD extensively
> for our work.
>
> I am trying to calculate the free energy profile of a cation along the
> normal to a specific site (COM of six atoms) on a solid substrate. Hence, i
> used distance Z and distance XY component for the CV analysis using
> harmonic constraints only for the distance Z components and for distance XY
> i have set the harmonic forceconstant to 0, but have applied lower and
> upper wall/boundary with force constant.
>
> I think in this way, the ion would explore a cylinder along the normal to
> the solid surface. Below is the config file i used for performing colvars
> module. The simulation runs fine without any issues.
>
> colvar {
> name pmf-dist
> width 0.4
> lowerboundary 1.0
> upperboundary 15.0
> expandboundaries off
>
> ###################### Component section ############################
> distanceZ {
> main {
> atomNumbers 3975
> }
> ref {
> atomNumbers 1384 1383 1374 1378 2262 2294
> }
> axis {
> (0.0, 0.0, -1.0)
> }
> forceNoPBC no
> oneSiteSystemForce no
> }
> outputValue on
> outputVelocity off
> outputSystemForce on
> outputAppliedForce on
> }
>
> colvar {
>
> name pmf-dist-xy
> width 0.4
>
> lowerboundary 0.0
> upperboundary 0.5
> expandboundaries off
> #lowerwall 0.0
> #lowerwallconstant 0.0
> upperwall 0.5
> upperwallconstant 0.7
>
> ###################### Component section ############################
>
> distanceXY {
> main {
> atomNumbers 3975
> }
> ref {
> atomNumbers 1384 1383 1374 1378 2262 2294
> }
> axis {
> (1.0, 1.0, 0.0)
> }
> forceNoPBC no
> oneSiteSystemForce no
> }
> outputValue on
> outputVelocity off
> outputSystemForce on
> outputAppliedForce on
> }
>
> harmonic {
> name umbrella-z
> colvars pmf-dist
> forceConstant 4.0
> centers 2.8
> }
> harmonic {
> name umbrella-xy
> colvars pmf-dist-xy
> forceConstant 0.0
> centers 0.0
> }
>
> However, when i view the trajectory file (dcd), the ion moves outside the
> boundary and wall constraints along XY and nevers comes back inside the
> cylinder. If i am correct, the term wall indicates a solid surface.
>
> My doubts are
> 1) why the ion is moving outside the wall eventhough there is a presence
> of upperwall force constant.
> 2) Does it indicate that the upperwall force constant value is not high
> enough to bring back the ion inside the cylinder. If that so, i have tried
> with high value but it is not working.
> 3) How can i probe the ion only inside the cylinder. Is there anything i
> am missing here.
>
> Could you please help me to solve the issue.
>
> Thanks in advance,
>
> Sincerely,
> Naresh
>
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