[gmx-users] umbrella sampling
Justin Lemkul
jalemkul at vt.edu
Fri Feb 2 16:31:14 CET 2018
On 2/2/18 8:43 AM, rose rahmani wrote:
> Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS
> simulation for each window.
>
>>> g_energy -f umbrella0.edr -o out.xvg
> 1 Bond 2 Angle 3 Proper-Dih. 4
> Improper-Dih.
> 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8
> Coulomb-(SR)
> 9 Coul.-recip. 10 COM-Pull-En. 11 Potential 12
> Kinetic-En.
> 13 Total-Energy 14 Conserved-En. 15 Temperature 16 Pressure
>
> 17 Constr.-rmsd 18 Vir-XX 19 Vir-XY 20 Vir-XZ
>
> 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
>
> 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
>
> 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
>
> 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36
> #Surf*SurfTen
> 37 Mu-X 38 Mu-Y
>
> 39 Mu-Z 40 Coul-SR:SOL-SOL
>
> 41 LJ-SR:SOL-SOL 42 Coul-14:SOL-SOL
>
> 43 LJ-14:SOL-SOL 44 Coul-SR:SOL-WAL
>
> 45 LJ-SR:SOL-WAL 46 Coul-14:SOL-WAL
>
> 47 LJ-14:SOL-WAL 48 Coul-SR:SOL-ZnS
>
> 49 LJ-SR:SOL-ZnS 50 Coul-14:SOL-ZnS
>
> 51 LJ-14:SOL-ZnS 52 Coul-SR:SOL-Protein
>
> 53 LJ-SR:SOL-Protein 54 Coul-14:SOL-Protein
>
> 55 LJ-14:SOL-Protein 56 Coul-SR:SOL-NA
>
> 57 LJ-SR:SOL-NA 58 Coul-14:SOL-NA 59 LJ-14:SOL-NA 60
> Coul-SR:SOL-CL
> 61 LJ-SR:SOL-CL 62 Coul-14:SOL-CL
>
> 63 LJ-14:SOL-CL 64 Coul-SR:SOL-wall0
>
> 65 LJ-SR:SOL-wall0 66 Coul-14:SOL-wall0
>
> 67 LJ-14:SOL-wall0 68 Coul-SR:SOL-wall1
>
> 69 LJ-SR:SOL-wall1 70 Coul-14:SOL-wall1
>
> 71 LJ-14:SOL-wall1 72 Coul-SR:WAL-WAL
>
> 73 LJ-SR:WAL-WAL 74 Coul-14:WAL-WAL
>
> 75 LJ-14:WAL-WAL 76 Coul-SR:WAL-ZnS
>
> 77 LJ-SR:WAL-ZnS 78 Coul-14:WAL-ZnS
>
> 79 LJ-14:WAL-ZnS 80 Coul-SR:WAL-Protein
>
> 81 LJ-SR:WAL-Protein 82 Coul-14:WAL-Protein
>
> 83 LJ-14:WAL-Protein 84 Coul-SR:WAL-NA
>
> 85 LJ-SR:WAL-NA 86 Coul-14:WAL-NA 87 LJ-14:WAL-NA 88
> Coul-SR:WAL-CL
> 89 LJ-SR:WAL-CL 90 Coul-14:WAL-CL
>
> 91 LJ-14:WAL-CL 92 Coul-SR:WAL-wall0
>
> 93 LJ-SR:WAL-wall0 94 Coul-14:WAL-wall0
>
> 95 LJ-14:WAL-wall0 96 Coul-SR:WAL-wall1
>
> 97 LJ-SR:WAL-wall1 98 Coul-14:WAL-wall1
>
> 99 LJ-14:WAL-wall1 100 Coul-SR:ZnS-ZnS
>
> 101 LJ-SR:ZnS-ZnS 102 Coul-14:ZnS-ZnS
>
> 103 LJ-14:ZnS-ZnS 104 Coul-SR:ZnS-Protein
>
> 105 LJ-SR:ZnS-Protein 106 Coul-14:ZnS-Protein
>
> 107 LJ-14:ZnS-Protein 108 Coul-SR:ZnS-NA
>
> 109 LJ-SR:ZnS-NA 110 Coul-14:ZnS-NA 111 LJ-14:ZnS-NA 112
> Coul-SR:ZnS-CL
> 113 LJ-SR:ZnS-CL 114 Coul-14:ZnS-CL
>
> 115 LJ-14:ZnS-CL 116 Coul-SR:ZnS-wall0
>
> 117 LJ-SR:ZnS-wall0 118 Coul-14:ZnS-wall0
>
> 119 LJ-14:ZnS-wall0 120 Coul-SR:ZnS-wall1
>
> 121 LJ-SR:ZnS-wall1 122 Coul-14:ZnS-wall1
>
> 123 LJ-14:ZnS-wall1 124 Coul-SR:Protein-Protein
>
> 125 LJ-SR:Protein-Protein 126 Coul-14:Protein-Protein
>
> 127 LJ-14:Protein-Protein 128 Coul-SR:Protein-NA
>
> 129 LJ-SR:Protein-NA 130 Coul-14:Protein-NA
>
> 131 LJ-14:Protein-NA 132 Coul-SR:Protein-CL
>
> 133 LJ-SR:Protein-CL 134 Coul-14:Protein-CL
>
> 135 LJ-14:Protein-CL 136 Coul-SR:Protein-wall0
>
> 137 LJ-SR:Protein-wall0 138 Coul-14:Protein-wall0
>
> 139 LJ-14:Protein-wall0 140 Coul-SR:Protein-wall1
>
> 141 LJ-SR:Protein-wall1 142 Coul-14:Protein-wall1
>
> 143 LJ-14:Protein-wall1 144 Coul-SR:NA-NA
>
> 145 LJ-SR:NA-NA 146 Coul-14:NA-NA 147 LJ-14:NA-NA 148
> Coul-SR:NA-CL
> 149 LJ-SR:NA-CL 150 Coul-14:NA-CL
>
> 151 LJ-14:NA-CL 152 Coul-SR:NA-wall0
>
> 153 LJ-SR:NA-wall0 154 Coul-14:NA-wall0
>
> 155 LJ-14:NA-wall0 156 Coul-SR:NA-wall1
>
> 157 LJ-SR:NA-wall1 158 Coul-14:NA-wall1
>
> 159 LJ-14:NA-wall1 160 Coul-SR:CL-CL 161 LJ-SR:CL-CL 162
> Coul-14:CL-CL
> 163 LJ-14:CL-CL 164 Coul-SR:CL-wall0
>
> 165 LJ-SR:CL-wall0 166 Coul-14:CL-wall0
>
> 167 LJ-14:CL-wall0 168 Coul-SR:CL-wall1
>
> 169 LJ-SR:CL-wall1 170 Coul-14:CL-wall1
>
> 171 LJ-14:CL-wall1 172 Coul-SR:wall0-wall0
>
> 173 LJ-SR:wall0-wall0 174 Coul-14:wall0-wall0
>
> 175 LJ-14:wall0-wall0 176 Coul-SR:wall0-wall1
>
> 177 LJ-SR:wall0-wall1 178 Coul-14:wall0-wall1
>
> 179 LJ-14:wall0-wall1 180 Coul-SR:wall1-wall1
>
> 181 LJ-SR:wall1-wall1 182 Coul-14:wall1-wall1
>
> 183 LJ-14:wall1-wall1 184 T-System
>
> 185 Lamb-System
>
> how can i understand that this 4nS simulation is enough for all 30 windows
> which i selected after pulling? as you see i'm doing NVT.i tried to
> calculate temperature(15) and total energy(13) and potential(11) for
> example for first window;
> Energy Average Err.Est. RMSD Tot-Drift
> ------------------------------------------------------------
> -------------------
> Potential -72708 9.2 227.038 -38.8081
> (kJ/mol)
> Total Energy -63763.9 8.7 273.747 -34.9771
> (kJ/mol)
> Temperature 299.977 0.022 5.04346 0.128492 (K)
> plots show that temperature is ok and total energy doesn't have
> considerable fluctuation (except after first moment). but potential
None of those values tell you anything about the convergence of your
simulations.
> fluctuates. since i don't see sharp peaks in PMF (but good trends), is it
> rational to do long time simulation? what is the main clue for knowing
> that? is it potential?
If you want to know if the PMF has converged, calculate it for
consecutive, non-overlapping time periods. If they are statistically
indistinguishable, you are done. If they are still changing over time,
you need longer runs.
> and what exactly total energy(13) refers to in my system?
Total energy = kinetic energy + potential energy. This is a basic
thermodynamic definition.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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