# Re: [gmx-users] umbrella sampling

```maybe this is irrelative but i expeienced in pulling that when i decrease
dt from 2fs to 1fs i could make AA much closer to Sheet (0.1 nm)in
comparison with 2fs(max 0.4 nm). it's normal but these pulling runs were
crushed before(when dt=2fs)  so i had had to decrease nsteps or decrease
pull_rate , but i don't face with these crush anymore! i can pull it too
close. i know maybe these beginner confessions seem unacceptable ;)))) and
silly.
i know this question is not accurate and can have many answers but, as a
professional and experienced person, would you please tell me, whenever you
face with  a crushed simulation, what will  you check?doubt? in your
system(separate of anything related to cpu&.... computers limitations) .
what cause simulations to be crushed usually?```
```
On Mon, Feb 5, 2018 at 12:05 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 2/4/18 3:25 PM, Rose wrote:
>
>> 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?
>>
>
> You can always decrease dt, that's "reasonable," but it makes no sense and
> is inefficient. Without any form of constraints, you'd likely be limited to
> dt = 0.0005 in many cases.
>
>
> -Justin
>
> 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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
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>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>>
>>>> --
>>> ==================================================
>>>
>>> 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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>>>
>>
> --
> ==================================================
>
> 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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