[gmx-users] umbrella sampling

Justin Lemkul jalemkul at vt.edu
Sun Feb 4 22:24:52 CET 2018



On 2/4/18 4:23 PM, Rose wrote:
> Oooh, i mean roomMate :)))
>
> Would you please answer my questions?

I already did. See my very detailed response below.

-Justin

> Sent from my iPhone
>
>> On Feb 5, 2018, at 0:48, Rose <rose.rhmn93 at gmail.com> wrote:
>>
>>
>> Sorry nothing mysterious,i'm rose(rose.rhmn93) in these all conversations, but i have some problems in my gmail which i can't open my emails every times(i don't why but it's sth related to country ip&...) because Of that i have to use my roomate account,sorrrry again
>>
>>
>> Sent from my iPhone
>>
>>> On Feb 5, 2018, at 0:35, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>> I don't know whether you're intentionally changing your email address or display name, but please refrain from doing so as it is very confusing who I'm talking to.
>>>
>>>> On 2/4/18 4:00 PM, Nick Johans wrote:
>>>> 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?
>>> If your simulation is crashing, you're doing something inappropriate, by causing particles to collide with one another. This is an entirely separate issue from the relationship between constraints and time step, dt. Your simulations are not unstable because of excessively fast bond vibrations, they're unstable because the nonbonded interactions in your system are unfavorable when allowed to run with dt = 2 fs.
>>>
>>> If the system is unstable at any point, you should verify the parametrization of any non-standard species, which in your case is the sheet. I recall long ago telling you this would be a challenging entity to parametrize, yet you quickly obtained a model and began using it. What verification did you perform to assure yourself that interactions of this ZnS sheet are reasonable in the context of protein moieties? Did you perform any QM interaction energies? Are there experimentally known binding free energies for model compounds? How do you know this model is appropriate?
>>>
>>> These are all things you need to consider, and questions that are not within the scope of this mailing list.
>>>
>>> -Justin
>>>
>>>>> On Mon, Feb 5, 2018 at 12:05 AM, Justin Lemkul <jalemkul at 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 <jalemkul at 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 <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
>>>>>>>>> <https://maps.google.com/?q=he+PMF+curves+and+if+they+are+overlapping&entry=gmail&source=g>
>>>>>>>>> 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.
>>>>>>>> --
>>>>>>> ==================================================
>>>>>>>
>>>>>>> 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.
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> 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.
>>> -- 
>>> ==================================================
>>>
>>> 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
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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

-- 
==================================================

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

==================================================



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