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.rhm...@gmail.com> wrote: > > > Sent from my iPhone > > > On Feb 2, 2018, at 19:01, Justin Lemkul <jalem...@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 > > > > jalem...@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-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? 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