<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div><br><br></div><div id="AppleMailSignature">Hi,</div><div id="AppleMailSignature"><br></div><div id="AppleMailSignature">Thanks!</div><div id="AppleMailSignature"><br></div><div id="AppleMailSignature">Regards</div><div id="AppleMailSignature">Jin</div><div><br>在 2016年10月5日,08:05,Berk Hess <<a href="mailto:hess@kth.se">hess@kth.se</a>> 写道:<br><br></div><blockquote type="cite"><div>
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<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>
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<blockquote cite="mid:CAGD4nqGCyPL3BuT-riJC15gqap4C=QFuX_pHux7ViF-gk6FtVw@mail.gmail.com" type="cite">
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<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>
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<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>
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