<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<div class="moz-cite-prefix">Hi,<br>
<br>
If you set an off-diagonal element in deform, you get shear flow.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 10/04/2016 07:40 PM, J Hu wrote:<br>
</div>
<blockquote
cite="mid:CAGD4nqGCyPL3BuT-riJC15gqap4C=QFuX_pHux7ViF-gk6FtVw@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<div dir="ltr">Hi Berk,
<div><br>
</div>
<div>Thanks for your advice! </div>
<div><br>
</div>
<div>However, I'm sorry that I do not really understand your
point... The deform md option should be turned off by default
right? So how could I adjust it to realize my implement of
shear flow? Could you please tell me some more details about
that if you are available? Thanks!</div>
<div><br>
</div>
<div>As for the patch, yes, I would really appreciate it if you
could share it with me!</div>
<div><br>
</div>
<div>Best wishes</div>
<div><br>
</div>
<div>Jin</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2016-10-04 14:22 GMT+01:00 Berk Hess <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div class="m_-4474147881397635249moz-cite-prefix">Hi,<br>
<br>
I think the defrom MD option can do what you want.<br>
It does not apply the proper SLLOD equations, but I
think this does not matter under most conditions. If you
want to use SLLOD, I have a patch for that.<br>
<br>
Cheers,<br>
<br>
Berk
<div>
<div class="h5"><br>
<br>
On 10/04/2016 03:06 PM, J Hu wrote:<br>
</div>
</div>
</div>
<div>
<div class="h5">
<blockquote type="cite">
<div dir="ltr">
<p
style="margin-top:0px;margin-bottom:0px;font-size:12pt"><i><font
face="comic sans ms, sans-serif">Hello,</font></i></p>
<p
style="margin-top:0px;margin-bottom:0px;font-size:12pt"><i><font
face="comic sans ms, sans-serif"><br>
</font></i></p>
<p
style="margin-top:0px;margin-bottom:0px;font-size:12pt"><font
face="comic sans ms, sans-serif"><i>I </i><i><i>have
recently </i>tried to simulate a shear
flow in a molecular dynamics model by
implementing the </i><i>Lees Edwards
boundary (periodic shear flow) conditions in
GROMACS. However the </i><i><i>results </i>I
got are strange ... <br>
<br>
</i></font></p>
<p
style="margin-top:0px;margin-bottom:0px;font-size:12pt"><font
face="comic sans ms, sans-serif"><i>I added
the effect of the shear,
delta_U(y)=gamma*dy, where gamma = dU/dy by
modifying the coordinate equation dx/dt =
... + gamma*dy in the x-direction so that
coordinate change along the x direction
becomes x(t+dt) = x(t) +
dt*[v(t) +gamma*dy]. The </i><i><i>calculation
of the molecular dynamics </i>velocity,
v(t) from the pair potential was kept the
same as usual from Newton's second law
without any change.<br>
</i></font></p>
<p
style="margin-top:0px;margin-bottom:0px;font-size:12pt"><i><font
face="comic sans ms, sans-serif"><br>
</font></i></p>
<font style="font-size:14px" face="comic sans ms,
sans-serif"><i style="color:rgb(51,51,51)">To
compare with the analytical shear flow
solution U(y), I then wrote a routine that
averages all atoms velocities in time as well
as in the homogeneuous x&z directions and
so obtained the velocity profile <span
style="font-size:16px">along the y-direction
(the velocity </span></i><i
style="color:rgb(51,51,51)"><span
style="font-size:16px"><i>information </i>was
directly obtained from the gro
files). However, strangely, the resulting
profile of the mean atom velocity, which I
expected to be flat around zero, turned out
to</span><span style="font-size:12pt"> have
a negative slope, -gamma, as if the model
tried to compensate for the positive shear
flow I was trying to impose. This effect is
very consistent for a range of different
shears -- from moderate to very small gamma.</span><span
style="font-size:12pt"> So I thought this is
due to the thermostat or some other
intrinsic GROMACS feature which checks the
atom velocities/deviations and </span></i><i
style="color:rgb(51,51,51)">holds the
velocities to correspond to the uniform state,
hence, creates an "anti-shear" effect.<br>
<br>
Did someone encounter a similar problem in
GROMACS and know how to disable these
stabilising features of </i><i
style="color:rgb(51,51,51)"><i>GROMACS</i>? <br>
Or, does someone know a simpler method how to
generated a shear flow in GROMACS ?</i><i
style="color:rgb(51,51,51)"><span
style="font-size:12pt"></span></i><span
style="color:rgb(51,51,51)"></span></font>
<p
style="margin-top:0px;margin-bottom:0px;font-size:12pt"><i><font
face="comic sans ms, sans-serif"><br>
</font></i></p>
<p
style="margin-top:0px;margin-bottom:0px;font-size:12pt"><i><font
face="comic sans ms, sans-serif">Thanks a
lot.</font></i></p>
<p
style="margin-top:0px;margin-bottom:0px;font-size:12pt"><i><font
face="comic sans ms, sans-serif"><br>
</font></i></p>
<p
style="margin-top:0px;margin-bottom:0px;font-size:12pt"><i><font
face="comic sans ms, sans-serif">Best wishes</font></i></p>
<p><i><br>
</i></p>
<p><i>Jin</i></p>
</div>
<br>
<fieldset
class="m_-4474147881397635249mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</div>
</div>
</div>
<br>
--<br>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List"
rel="noreferrer" target="_blank">http://www.gromacs.org/<wbr>Support/Mailing_Lists/GMX-<wbr>developers_List</a>
before posting!<br>
<br>
* Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
rel="noreferrer" target="_blank">http://www.gromacs.org/<wbr>Support/Mailing_Lists</a><br>
<br>
* For (un)subscribe requests visit<br>
<a moz-do-not-send="true"
href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers"
rel="noreferrer" target="_blank">https://maillist.sys.kth.se/<wbr>mailman/listinfo/gromacs.org_<wbr>gmx-developers</a>
or send a mail to <a moz-do-not-send="true"
href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@<wbr>gromacs.org</a>.<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>