ABF - distance between two domains

From: Nadeem A. Vellore (vnadeem_at_gmail.com)
Date: Wed Feb 27 2013 - 15:12:35 CST

Hi,

I am trying to use ABF using NAMD2.9. I am trying to use the distance
between two set of atoms as my constrain term. I am trying to setup by
forcing the initial simulation with higher wallconstant to reach a given
distance. Once it reaches the point (101-103 Angstrom), I want to start ABF
freshly again. Currently the distance is around 110. Below is the
Distance.in script used.

Issue : After few thousand steps, I look into the colvars.traj file and I
see that the distance is fluctuating around 102-103, which I am glad.
however, when I see the trajectory in VMD and calculate the distance
between these two group of atoms using VMD, the values are still in 109 and
110. I am not sure about the origin of this discrepancy. Is there a limit
in the number of atoms defined in the group1/2 segment. Am I doing
something wrong.

File : Distance.in
----------------------
colvarsTrajFrequency 2000
colvarsRestartFrequency 20000

colvar {
   name COMDistance
  width 0.1
  lowerboundary 101.0
  upperboundary 103.0

  lowerwallconstant 50.0
  upperwallconstant 50.0

  distance {
    group1 {
                 atomnumbers 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73
74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98
99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117
118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136
}
group2 {
               atomnumbers 11589 11590 11591 11592 11593 11594 11595 11596
11597 11598 11599 11600 11601 11602 11603 11604 11605 11606 11607 11608
11609 11610 11611 11612 11613 11614 11615 11616 11617 11618 11619 11620
11621 11622 11623 11624 11625 11626 11627 11628 11629 11630 11631 11632
11633 11634 11635 11636 11637 11638 11639 11640 11641 11642 11643 11644
11645 11646 11647 11648 11649 11650 11651 11652 11653 11654 11655 11656
11657 11658 11659 11660 11661 11662 11663 11664 11665 11666 11667 11668
11669 11670 11671 11672 11673 11674 11675 11676
}
}

abf {
colvars COMDistance
fullSamples 1000
hideJacobian
}

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