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<div class="moz-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<br>
<br>
On 10/04/2016 03:06 PM, J Hu wrote:<br>
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cite="mid:CAGD4nqG0vzJM07Hv1DZ4cTKPm52SYF2B2FToU--GNCdEWyigkQ@mail.gmail.com"
type="cite">
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<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
style="margin-top:0px;margin-bottom:0px;font-family:'microsoft
yahei ui','microsoft
yahei',微软雅黑,simsun,宋体,sans-serif;font-size:12pt"><i><br>
</i></p>
<p
style="margin-top:0px;margin-bottom:0px;font-family:'microsoft
yahei ui','microsoft
yahei',微软雅黑,simsun,宋体,sans-serif;font-size:12pt"><i>Jin</i></p>
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