[gmx-users] umbrella sampling

Rose rose.rhmn93 at gmail.com
Sun Feb 4 19:56:39 CET 2018


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)


Sent from my iPhone

> On Feb 4, 2018, at 17:00, Justin Lemkul <jalemkul at 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 <jalemkul at 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
> 
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> 
> ==================================================
> 
> -- 
> 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-request at gromacs.org.


More information about the gromacs.org_gmx-users mailing list