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
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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
==================================================
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Gromacs Users mailing list
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/Mailing_Lists/GMX-Users_List before posting!
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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
==================================================
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