[gmx-users] umbrella sampling
Rose
rose.rhmn93 at gmail.com
Sun Feb 4 21:25:30 CET 2018
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?
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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or 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
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list