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> 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
> 
> ==================================================
> 
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