From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Mon Mar 18 2013 - 12:14:46 CDT
Hi all,
I am using collective variable analysis module in NAMD to get PMF profile.
I am quite new to collective variable analysis module in NAMD.
I am trying to calculate the free energy profile of an ion along the normal to specific site (COM of six atoms) on a solid substrate.
Hence, i used distanceZ component (Projection of a vector to an axis)for the CV analysis method using harmonic constraints.
Below is the configuration file i used for CV module. The simulations runs fine and i have the PMF.
CV module
colvar {
name pmf-dist
width 0.2
lowerboundary 1.0
upperboundary 15.0
expandboundaries off
distanceZ {
main {
atomNumbers 1512
}
ref {
atomNumbers 1375 1467 1406 1385 1384 1396
}
axis {
(0.0, 0.0, -1.0)
}
forceNoPBC no
oneSiteSystemForce no
}
outputValue on
outputVelocity off
outputSystemForce on
outputAppliedForce on
}
Constraints
harmonic {
name umbrella
colvars pmf-dist
forceConstant 2.0
centers 8.0
}
However, when i try to view the trajectory files(*.dcd), the results are quite different.
For instance, the distance between the main and ref group is fine on Z -axis.
However, during the course of the simulation, the vector moves along the XY plane at the centered Z-position.
I understand that only the Z component is constrained and not XY.
My doubts are
1) why the vector is moving along the XY plane when the axis keyword for x and y are set to be 0.0
2) Since, there is a constant movement along the XY plane, does it still hold the atom identities for distance measurements.
3) I think that this motion has a strong influence on sampling the regions specific to the defined sites.
4) how to avoid this and to keep the XY motions to minimum and to have calculate the PMF for the specified sites on the substrate.
Could you please help me in this regard
Thanks in advance
Sincerely,
Naresh
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