From: Nadeem A. Vellore (vnadeem_at_gmail.com)
Date: Wed Feb 27 2013 - 15:45:49 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.
Thanks
Nadeem
>
> 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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