[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
>>>
>>> * 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-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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