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On 23/06/2011 12:38 PM, xiaodong huang wrote:
<blockquote
cite="mid:BANLkTikpdN6nGADhm=mYKHwKB2qyKUNLxw@mail.gmail.com"
type="cite">
<div>Dear Justin and gmxers</div>
<div>Thank you so much for your helpful hints, but I am wondering
how to check if I have </div>
<div>obtained "proper distributions for the desired ensemble", as
suggested in your email?</div>
<div>My thoughts are:</div>
<div>1. As for NVT ensemble, I need to check if the velocity (or
speed) of molecules in my simulation</div>
<div> follows a Maxwell-boltzmann distribution, and the
velocity is for the center of mass of these </div>
<div> molecules, not for individual atoms, right?</div>
</blockquote>
<br>
Atoms are physical. Molecules are a convenient grouping of them to
aid human understanding.<br>
<br>
<blockquote
cite="mid:BANLkTikpdN6nGADhm=mYKHwKB2qyKUNLxw@mail.gmail.com"
type="cite">
<div>2. Can I also check the distribution of T in my simulation (I
output T every 100 steps or so, and </div>
<div> make a statistics)? It is said in NVT ensemble, T follows
a gaussian distribution, according</div>
<div> to central limit theorem, and the square of its variance
is 2T*T/(3N). Is that correct?</div>
</blockquote>
<br>
g_energy will report some descriptive statistics.<br>
<br>
<blockquote
cite="mid:BANLkTikpdN6nGADhm=mYKHwKB2qyKUNLxw@mail.gmail.com"
type="cite">
<div>3. As for NPT ensemble, how to check if I have get a
correction distribution from pressure</div>
<div> coupling? Can I also check the P or V distribution? If
so, what is the correct distribution I </div>
<div> should get? I find some clues at "Understanding Modern
Molecular Dynamics </div>
<div> J. Phys. Chem. B 2000, 104, 159-178", but this paper just
discuss some simple systems</div>
<div> in T,P coupling section, and I still do not know the
correct distribution I should</div>
<div> get for my own simulations (e.g. protein in a box of
water, NPT).</div>
</blockquote>
<br>
You need to use a small system that you can exhaustively sample,
deduce what the statistical distribution of your observables should
be, and see what you get. Or you can simply rely on the use of
algorithms that have been shown to produce correct distributions,
and trust/verify that GROMACS has implemented them correctly.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTikpdN6nGADhm=mYKHwKB2qyKUNLxw@mail.gmail.com"
type="cite">
<div>4.Are there any other quantities I need to check to make sure
I have sampled a correct </div>
<div> ensemble? I think to check the distribution of v, T, P V
should be enough for this purpose,</div>
<div> lthough to check more quantities is a plus, right?</div>
<div>Any suggestions or comments are very welcome. Thank you.</div>
<div>yours</div>
<div>xiaodong</div>
<div>Research School of Chemistry<br>
ANU<br>
<br>
</div>
<div class="gmail_quote">On Tue, Jun 21, 2011 at 11:21 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204, 204);
margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote">
<div class="im"><br>
<br>
xiaodong huang wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204,
204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote">Dear gromacs-ers<br>
<br>
I am using stochastic dynamics integrator (integrator =
sd), so most of the time, I only need to adjust following
parameters for temperature and pressure coupling: tau_t
pcoupl tau_p (ref_t is room temperature and ref_p is 1
atm, compressibility can be taken from experimental
numbers).<br>
<br>
<br>
In the manual, a tau_t between 1 and 2ps is recommended
for the sake of simulation stability, but I see someone
use a tau_t of 0.1ps with the same integrator (integration
was performed with Langevin dynamics,49 with a reference
temperature of 300 K and a weak frictional constant of 10
ps-1,) when simulating water solvent. I also see someone
use a tau_t of 0.2ps with the same integrator (To obtain a
isothermal–isobaric ensemble at 293 K, a leap-frog
stochastic dynamics integrator16 was used to integrate the
equations of motion. The inverse friction constant was set
to 0.2 ps.) when simulating some organic solvent. I check
the references mentioned in these gromacs papers so I am
pretty sure they are using the same integrator. So I am a
bit confusing here, what tau_t should I use, the number
between 1 and 2ps as recommended by the manual, or the
numbers below 1ps, as reported in these papers? Does this
parameter depend on what solvent (water, cyclohexane) I
use? Can I just use any number between 0.1ps and 2ps and
check if my simulations look fine or there is some ‘best’
number for a particular solvent?<br>
<br>
</blockquote>
<br>
</div>
This was discussed recently:<br>
<br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/2011-June/061992.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-June/061992.html</a>
<div class="im"><br>
<br>
<blockquote style="border-left: 1px solid rgb(204, 204,
204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote"> <br>
When I use berendsen or Parrinello-Rahman, the same
questions apply: Is there some ‘best’ number for a
particular solvent, or I can just use any number between
0.5ps and 5ps and check if my simulations run well?<br>
<br>
<br>
When I read papers, I find many different pressure
coupling constant (tau_p) ranging from 0.5ps to 1ps
(water), 1ps to 5ps (organic solvent) with weak coupling
scheme in gromacs. I am wondering why they use bigger
number for organic solvent? If I use Parrinello-Rahman (it
is said to be better than berendsen in the manual), do I
need to change tau_p, or I can just use the same tau_p as
berendsen?<br>
<br>
</blockquote>
<br>
</div>
Time constants are a bit empirical. The Berendsen algorithm
is more forgiving; it relaxes very quickly and thus low values
of tau_t/tau_p are stable. For methods that allow for wider
oscillations (N-H for temperature, P-R for pressure), small
tau_t/tau_p values are unstable due to the nature of these
algorithms. The most important information is whether or not
you obtain proper distributions for the desired ensemble. Any
algorithm can be made to behave artificially rigorously or
artificially relaxed.<br>
<br>
-Justin
<div class="im"><br>
<br>
<blockquote style="border-left: 1px solid rgb(204, 204,
204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote">Thank you so much for your kind help,
any suggestions or clues are very welcome.<br>
<br>
Yours<br>
<br>
xiaodong huang<br>
Research School of Chemistry<br>
ANU<br>
<br>
</blockquote>
<br>
</div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu/"
target="_blank">vt.edu</a> | <a moz-do-not-send="true"
href="tel:%28540%29%20231-9080" target="_blank"
value="+15402319080">(540) 231-9080</a><br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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