From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Thu Dec 10 2020 - 13:01:48 CST
In the plot, the PMF (kcal/mol, vertical axis) is calculated versus
distance (A, horizontal axis).
All the best,
Zeynab
On Thu, 10 Dec 2020, 22:25 zeynab hosseini, <hosseinizeynab93_at_gmail.com>
wrote:
> Dear All,
>
> I have performed 500ns of well-tempered metadynamics (wt-mtd) simulation
> to calculate the potential of mean force (PMF) over the adsorption of a
> small molecule on an infinite cabon nanotube surface (NAMD 2.13b1). The CNT
> is oriented along the z-axis and the reaction coordinate is the radial
> distance of molecule from the CNT central axis. The lowerboundary and
> upperboundary are considered to be 4A and 30.5A, respectively. I have
> plotted the PMF versus radial distance over 500ns (black curve), 496ns
> (red), 492ns (green), 488ns (blue) and 484ns (yellow) of wt-mtd simulation (
> link
> <https://drive.google.com/file/d/1qaJmUTdVBsy6iEZoXTcR0W7Aj9u_uVp5/view?usp=sharing>).
> The Jacobian term of the PMF (-kB T ln(r)) is included in the plot, too.
>
> I wonder if I can conclude the PMF is converged after 500ns. After about
> 450ns, the PMF plot does not show any significant change from the plot I've
> already attached. If so, then is that correct to calculate the average of
> the five mentioned PMF curves as the final PMF, along with the standard
> deviation to be considered as the error bar?
>
> Is there any way to get more accurate PMF, e.g. all five curves overlap
> each other entirley? Should I change the reaction coordinate or is there
> any other way?
>
> Is there anyway to get faster converngence? e.g. much shorter than 500ns.
> For example to reduce the upperboundary from 30.5A to 20A? I'm not sure if
> it affect the convergence positively.
>
> Since the CNT and water box are symmetrical (CNT+molecule are solvated in
> a water box of 70A × 70A × 24A), I wonder if I can confine the molecule
> movements into a specific region, in order to get faster convergence. I
> mean, e.g., if the CNT length is 20A (-10A < z < 10A), we apply restraints
> to limit the molecule movements only in a region with -5A < z < 5A ? Does
> it help to converge faster without affecting the physics of the system?
>
>
> I would really appreciate if anybody guides me..
>
> All the Best,
> Zeynab
>
> The relevant part of the metadynamics configuration file:
> colvarsTrajFrequency 500
> colvarsRestartFrequency 1000
>
> colvar {
> name Translocation
>
> upperboundary 30.5
> lowerboundary 4.0
> upperWallConstant 100.0
> lowerWallConstant 100.0
> width 0.125331414
>
> distanceXY {
> main {
> atomnumbers { 165 }
> }
> ref {
> atomnumbers {
> 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
> }
> }
> axis ( 0.0, 0.0, 1.0 )
> }
> }
>
>
> metadynamics {
> name meta-distance
> colvars Translocation
> hillWeight 0.01
> newHillFrequency 250
> dumpFreeEnergyFile yes
> writeHillsTrajectory on
> hillwidth 1.253314137
> wellTempered on
> # bias factor=6
> biasTemperature 1550
>
>
> }
>
>
>
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