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 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? and what exactly total energy(13) refers to in my system? would you please help me? Thank you for your all considerations -- 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.