[gmx-users] umbrella sampling
rose rahmani
rose.rhmn93 at gmail.com
Fri Feb 2 14:44:00 CET 2018
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
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