Re: ABF - using gyration

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Tue Oct 28 2008 - 11:52:49 CDT

Hi Vaithee,
Can you compute a local PMF around the minimum from your unbiased
simulation, and compare it with what the ABF runs measure?
Best,
Jerome

On Tue, Oct 28, 2008 at 11:18 AM, Subramanian Vaitheeswaran
<vaithee_at_umd.edu> wrote:
> Dear Chris and Jerome,
>
> I am trying to use ABF to calculate the PMF of a peptide with the radius of gyration as the order parameter. But my system is behaving strangely.
>
> I first ran the system (a decapeptide in a box of water) in NAMD *without* any biasing and measured the radius of gyration, rg to be in the range [6.0,7.5]. I then used ABF with "coordinate gyration" with the same range, expecting to see sampling in this region. But xi, the order parameter, rapidly drops to ~5.6.
>
> Next, I reduced range to [5.4,5.8] - then xi drops to ~5.4. So, the biasing seems to be driving the system opposite to the desired direction. This is the ABF part of my conf file:
> **************************
> if {1} {
> source ~/NAMD_2.6_Linux-i686/lib/abf/abf.tcl
> abf coordinate gyration
> abf abf1 {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169}
> abf dxi 0.05
> abf xiMin 5.4
> abf xiMax 5.8
> abf writeXiFreq 5000
> abf outFile rg.pmf
> abf historyFile rg.hist
> abf fullSamples 200
> abf inFiles {./1_5ns/rg.pmf}
> abf dSmooth 0.0
> }
> **************************
> Both ABF runs were ~2ns long at a 2fs time step. What could be going wrong?
>
> thanks,
> Vaithee
> ============================================
> S. Vaitheeswaran
> Post-doctoral Research Associate
> Institute for Physical Science & Technology
> Rm 2116, Bldg. 85
> University of Maryland
> College Park MD 20742
> email: vaithee_at_umd.edu
> Phone: 301-405-7568
> ============================================
>
>

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