<div dir="ltr"><div><div>Dear Mattioli,<br></div>You are right and I strongly agree with you DFT is capable of providing a universally-agreed on framework to deal with the temperature dependence of liquid water via the CPMD technique. What I am trying to say is that simulating an aqueous solution by a triclinic Bravais lattice--as is demonstrated in the example--is not but a simple, imprecise approximation. And no one can provide a better, more precise picture within QE.<br></div><div><div><div><div class="gmail-Iyc gmail-d-k-l"> </div></div></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px">Regards,<br></span></span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px">Ashkan</span><i style="font-size:12.8px"><br><br></i></span></span></div><div><font size="2"><b><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Ashkan Shekaari</span></span></b></font></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Plasma Physics Research Center</span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px"><span style="font-size:12.8px">Science and Research Branch</span></span></span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">I A U, <span style="font-size:12.8px">14778-93855 Tehran, Iran.</span></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Sat, May 6, 2017 at 1:27 PM, ashkan shekaari <span dir="ltr"><<a href="mailto:shekaari@gmail.com" target="_blank">shekaari@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">To the best of my knowledge, David could examine only the atomic structure of the solute using high-performance computer clusters supposing that the solute is made of not a large number of atoms and he has to write on his own several codes in order to obtain the temperature dependence of some phase transition indicators such as mean-square displacements and the Lindemann index.<br></div><div class="gmail_extra"><span class=""><br clear="all"><div><div class="m_5360044084451608129gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px">Regards,<br></span></span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px">Ashkan</span><i style="font-size:12.8px"><br><br></i></span></span></div><div><font size="2"><b><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Ashkan Shekaari</span></span></b></font></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Plasma Physics Research Center</span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px"><span style="font-size:12.8px">Science and Research Branch</span></span></span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">I A U, <span style="font-size:12.8px">14778-93855 Tehran, Iran.</span></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br></span><div><div class="h5"><div class="gmail_quote">On Sat, May 6, 2017 at 1:17 PM, ashkan shekaari <span dir="ltr"><<a href="mailto:shekaari@gmail.com" target="_blank">shekaari@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Actually, I have recently published a paper on melting behavior of some graphene quantum dots containing 6 and 10 atoms, but I had to write on my own more than 800 program lines in bash and fortran for such small-sized structures to get my desired results. And it is based on such an experience that I believe QE is not that sophisticated in DFMD calculations of large, non-solid, molecular structures. Even if you are a highly-experienced programmer, you cannot get the desired results conclusively as the number of atoms increases to form a solution.<br></div><div class="gmail_extra"><span><br clear="all"><div><div class="m_5360044084451608129m_7262021426938114509gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px">Regards,<br></span></span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px">Ashkan</span><i style="font-size:12.8px"><br><br></i></span></span></div><div><font size="2"><b><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Ashkan Shekaari</span></span></b></font></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Plasma Physics Research Center</span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px"><span style="font-size:12.8px">Science and Research Branch</span></span></span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">I A U, <span style="font-size:12.8px">14778-93855 Tehran, Iran.</span></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br></span><div><div class="m_5360044084451608129h5"><div class="gmail_quote">On Sat, May 6, 2017 at 1:00 PM, ashkan shekaari <span dir="ltr"><<a href="mailto:shekaari@gmail.com" target="_blank">shekaari@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Dear <span name="Giuseppe Mattioli" class="m_5360044084451608129m_7262021426938114509m_1519142380172199998gmail-gD">Mattioli,<br><br></span></div><span name="Giuseppe Mattioli" class="m_5360044084451608129m_7262021426938114509m_1519142380172199998gmail-gD">Water is not a crystal and therefore it cannot be treated as a periodic str</span>ucture. The aforementioned example provides only a naive picture of water as an aqueous compartment leading to a crude approximation of the given system as well. Moreover, QE is not best suited for DFMD simulations of large, nonperiodic, liquid systems. <br></div><div class="gmail_extra"><br clear="all"><div><div class="m_5360044084451608129m_7262021426938114509m_1519142380172199998gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px">Regards,<br></span></span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px">Ashkan</span><span class="m_5360044084451608129m_7262021426938114509HOEnZb"><font color="#888888"><i style="font-size:12.8px"><br><br></i></font></span></span></span></div><span class="m_5360044084451608129m_7262021426938114509HOEnZb"><font color="#888888"><div><font size="2"><b><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Ashkan Shekaari</span></span></b></font></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Plasma Physics Research Center</span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span style="font-size:12.8px"><span style="font-size:12.8px">Science and Research Branch</span></span></span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">I A U, <span style="font-size:12.8px">14778-93855 Tehran, Iran.</span></span></span></div></font></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div><div><div class="m_5360044084451608129m_7262021426938114509h5">
<br><div class="gmail_quote">On Sat, May 6, 2017 at 12:21 PM, Giuseppe Mattioli <span dir="ltr"><<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Dear David and Ashkan<br>
<span><br>
> You cannot simulate the system as periodic. You have to use a large super<br>
> cell with vacuum spaces along the three spatial directions. Moreover, you<br>
> can simulate the solution only via importing a large number of atomic<br>
> positions of the order of 25000 at least, which does not seem to be<br>
> feasible by QE even in case of using random generators unless you have a<br>
> supercomputer facility.<br>
<br>
</span>This comments are misleading, if not wrong in some cases.<br>
First of all you can for sure perform ab initio molecular dynamics<br>
(aimd) simulations of a water solution in a periodic box, and you do<br>
not need a huge number of atoms. One of the cp.x examples provides<br>
starting points, see here<br>
/Your_Path_To_Espresso_6.1/Exa<wbr>mples/CPV/example04<br>
<span><br>
>> Does anyone know of examples, benchmarks, or recommendations? Would the<br>
>> X.blyp-van.ak pseudopotentials be appropriate? Any guidance or advice<br>
>> about parameter settings for this application would be much appreciated<br>
<br>
</span>Yes, you can use ultrasoft pseudopotentials such as X.blyp-van.ak.<br>
They used to be old and well-tested vanderbilt ultrasoft<br>
pseudopotentials generated many years ago by Axel Kohlmeyer (ak). But<br>
if you are not familiar with this terminology (ultrasoft,<br>
norm-conserving, van, mt, rrkj, paw, ...) you should start with some<br>
tutorial on pseudopotentials, because you must be sure to use<br>
converged plane-wave and density cutoffs for a given set of<br>
pseudopotentials.<br>
<br>
There is a very large number of options that must be set in the cp.x<br>
input. I cannot review them here. But there are also tons of<br>
literature on aimd simulations of water solutions, and you will easily<br>
find something that will help to choice a lot of parameters (box<br>
dimensions, NVT, NVP, NVE dynamics, thermostats, ...)<br>
<span><br>
> Indeed, QE is not best suited for MD simulations and I strongly recommend<br>
> the gromacs package.<br>
<br>
</span>Of course Ashkan might be right on a couple of points: if you have<br>
very big molecules weakly interacting with the solvent, and you are<br>
interested in the morphology of the solute only, then you have to<br>
perform very long md simulations and to use a large number of water<br>
molecules, and this might be costly and time-consuming if performed at<br>
an aimd level. If you want to study proton exchanges, reactions,<br>
dipole dynamics, ... you need aimd. You surely know whether your<br>
scientific task strictly requires aimd rather than model-potential md.<br>
<br>
HTH<br>
Giuseppe<br>
<span><br>
Quoting ashkan shekaari <<a href="mailto:shekaari@gmail.com" target="_blank">shekaari@gmail.com</a>>:<br>
<br>
> Indeed, QE is not best suited for MD simulations and I strongly recommend<br>
> the gromacs package.<br>
<br>
</span><div><div class="m_5360044084451608129m_7262021426938114509m_1519142380172199998h5">> You cannot simulate the system as periodic. You have to use a large super<br>
> cell with vacuum spaces along the three spatial directions. Moreover, you<br>
> can simulate the solution only via importing a large number of atomic<br>
> positions of the order of 25000 at least, which does not seem to be<br>
> feasible by QE even in case of using random generators unless you have a<br>
> supercomputer facility.<br>
><br>
> On May 6, 2017 9:09 AM, "D J Anick" <<a href="mailto:david.anick@rcn.com" target="_blank">david.anick@rcn.com</a>> wrote:<br>
><br>
>> Hello plane wavers,<br>
>><br>
>> I am interested in using QE for a molecular dynamics simulation of an<br>
>> aqueous solution containing a solute, modeling it as a 3-D periodic cell.<br>
>> Principal questions would be about solvation shell geometries, distribution<br>
>> of configurations adopted by the solute, and H-bond duration / stability.<br>
>><br>
>> Does anyone know of examples, benchmarks, or recommendations? Would the<br>
>> X.blyp-van.ak pseudopotentials be appropriate? Any guidance or advice<br>
>> about parameter settings for this application would be much appreciated.<br>
>><br>
>> Thank you in advance,<br>
>> David Anick<br>
>> david.anick###<a href="http://rcn.com" rel="noreferrer" target="_blank">rcn.com</a><br>
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