[gmx-users] umbrella sampling
Justin Lemkul
jalemkul at vt.edu
Sun Feb 4 21:00:30 CET 2018
On 2/4/18 1:56 PM, Rose wrote:
> Thank you so much,
> Is it difference between using gmx tpbconv -extend 5ps OR use .gro file of last simulation as an input For new 5nS simulation?(continiuation=yes in .mdp file)
The only reason to invoke grompp is if you're changing something about
the system. For a simple continuation use tpbconv/convert-tpr and mdrun
-cpi.
-Justin
>
> Sent from my iPhone
>
>> On Feb 4, 2018, at 17:00, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>>> 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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--
==================================================
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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