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.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

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

Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

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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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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