[gmx-users] umbrella sampling
Justin Lemkul
jalemkul at vt.edu
Sun Feb 4 21:36:04 CET 2018
On 2/4/18 3:25 PM, Rose wrote:
> Jeah,i meant grompp :)))
> and last question, i set constraint = h-Bonds, and dt=0.002 because Of that(since usually h-Bonds have Max frequency and.... if i assume them constraint so it's not reasonable to set dt=0.001 ) , is this assumption true?
You can always decrease dt, that's "reasonable," but it makes no sense
and is inefficient. Without any form of constraints, you'd likely be
limited to dt = 0.0005 in many cases.
-Justin
> Sent from my iPhone
>
>> On Feb 4, 2018, at 23:30, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>>> 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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>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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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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