Oooh, i mean roomMate :)))

Would you please answer my questions?

Sent from my iPhone

> On Feb 5, 2018, at 0:48, Rose <rose.rhm...@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 <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
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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
>>>>>> 
>>>>>> ==================================================
>>>>>> 
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>> 
>>>>>> * Please search the archive at http://www.gromacs.org/Support
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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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>>>> 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
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