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 <jalem...@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 <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
>>>>>>> <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
>>>>>>> 
>>>>>>> jalem...@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-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
>>>>> 
>>>>> ==================================================
>>>>> 
>>>>> --
>>>>> 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-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
>>> 
>>> ==================================================
>>> 
>>> --
>>> 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-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
> 
> ==================================================
> 
> -- 
> 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-requ...@gromacs.org.
-- 
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-requ...@gromacs.org.

Reply via email to