[gmx-users] umbrella sampling
Nick Johans
johans.nick93 at gmail.com
Sun Feb 4 22:00:41 CET 2018
maybe this is irrelative but i expeienced in pulling that when i decrease
dt from 2fs to 1fs i could make AA much closer to Sheet (0.1 nm)in
comparison with 2fs(max 0.4 nm). it's normal but these pulling runs were
crushed before(when dt=2fs) so i had had to decrease nsteps or decrease
pull_rate , but i don't face with these crush anymore! i can pull it too
close. i know maybe these beginner confessions seem unacceptable ;)))) and
silly.
i know this question is not accurate and can have many answers but, as a
professional and experienced person, would you please tell me, whenever you
face with a crushed simulation, what will you check?doubt? in your
system(separate of anything related to cpu&.... computers limitations) .
what cause simulations to be crushed usually?
On Mon, Feb 5, 2018 at 12:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>>> <https://maps.google.com/?q=he+PMF+curves+and+if+they+are+overlapping&entry=gmail&source=g>
>>>>> 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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>> --
>>> ==================================================
>>>
>>> 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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
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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
>
> ==================================================
>
> --
> Gromacs Users mailing list
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