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)
Sent from my iPhone > On Feb 4, 2018, at 17:00, Justin Lemkul <jalem...@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 <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? > > 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 > > 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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