Jeah,i meant grompp :)))
and last question, i set constraint = h-Bonds, and dt=0.002 because Of  
that(since usually h-Bonds have Max frequency and.... if i assume them 
constraint so it's not reasonable to set dt=0.001 ) , is this assumption true?

Sent from my iPhone

> On Feb 4, 2018, at 23:30, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
>> On 2/4/18 1:56 PM, Rose wrote:
>> 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)
> 
> The only reason to invoke grompp is if you're changing something about the 
> system. For a simple continuation use tpbconv/convert-tpr and mdrun -cpi.
> 
> -Justin
> 
>> 
>> 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
>>> 
>>> ==================================================
>>> 
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>>> Gromacs Users mailing list
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> 
> -- 
> ==================================================
> 
> 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
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