[gmx-users] umbrella sampling
Nick Johans
johans.nick93 at gmail.com
Fri Feb 2 17:00:20 CET 2018
and i have AA between sheet and wall.and it should get closer to sheet
during pulling. How should i set the initial place of amino acid? it should
have the minimum interaction with wall and sheet , am i right?
On Fri, Feb 2, 2018 at 7:14 PM, Rose <rose.rhmn93 at gmail.com> 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?
> What do you mean "statistically", would you please give me an example?
> Thank you so much
>
> >> and what exactly total energy(13) refers to in my system?
> >
> > Total energy = kinetic energy + potential energy. This is a basic
> thermodynamic definition.
> >
> > -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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