Collective variable module

From: naresh kumar (naresh.cmds_at_gmail.com)
Date: Thu Apr 10 2014 - 11:36:07 CDT

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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