[gmx-users] umbrella sampling
Justin Lemkul
jalemkul at vt.edu
Sun Feb 4 14:31:10 CET 2018
On 2/2/18 10:44 AM, Rose wrote:
>
> Sent from my iPhone
>
>> On Feb 2, 2018, at 19:01, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>>> 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.
> You mean i should use the output Of 4nS simulation, as an input for,for example next 10nS and at the end i have simulated it for 14nS,yes?
I don't have any idea about what arbitrary amount of time you should
target for your simulation, but you need to let convergence testing be
your guide.
> What do you mean "statistically", would you please give me an example?
Use the bootstrapping method of gmx wham to produce error estimates.
Then plot the PMF curves and if they are overlapping within error, then
you have an argument for convergence.
-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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