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<div class="moz-cite-prefix">I want it more like the freeze groups,
but moving. It should be used like a frozen layer stabilizing a
thin layer of solids, but with a constant velocity. <br>
</div>
<div class="moz-cite-prefix">It's partly working, but I wasn't able
to make a good (reasonable fast) build and installation on our HPC
system, so I want to switch to easybuild and patching a version
which is supported (max. 2019.4). As the way groups are defined
was changed between 2016.3 and 2019.6 I'm thinking about trying to
use one of the already defined groups to avoid problems with that.</div>
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<div class="moz-cite-prefix">Am 10.04.20 um 23:30 schrieb Erik
Lindahl:<br>
</div>
<blockquote type="cite"
cite="mid:CAEJJM8HYAS_Z1qYof6EQTFYa+ijp88HwgYxhkaG+Yb-DTQbbVw@mail.gmail.com">
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<div dir="ltr">That does make sense, and was actually how I recall
the implementation, but sadly it's not reflected in the
documentation. That says quite explicitly all atoms in the group
will experience constant acceleration, not merely have an
acceleration factor added.
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Erik </div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Apr 10, 2020 at 11:01
PM Berk Hess <<a href="mailto:hess@kth.se"
moz-do-not-send="true">hess@kth.se</a>> wrote:<br>
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<div>
<div>Hi,<br>
<br>
Acceleration groups will not work as those add an extra
force to a group and do not keep the total acceleration
constant.<br>
<br>
I think that using a pull coordinate with absolute
reference and of constraint type should work, then you
need to set a velocity using the free-energy coupling with
lambda and setting a pull rate.<br>
<br>
Otherwise you can indeed use one of the two user groups.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2020-04-10 13:01, Erik Lindahl wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Rebecca,
<div><br>
</div>
<div>I have to confess it was a _long_ time since I
looked into these parts of the code, but you might be
able to achieve this simply by defining a group,
giving it the initial velocity you want, and then
using the constant-acceleration functionality with the
value 0.0 (since zero constant acceleration means
constant speed).</div>
<div><br>
</div>
<div>And if that fails, it should be possible to fix it
without too much effort :-)</div>
<div><br>
</div>
<div>Otherwise, the idea of the user groups is exactly
that you should be able to quickly implement a small
routine where you do something to an arbitrary group
without having to redefine the input mdp options,
create a new (incompatible) TPR version, and also
having to modify the enum lists.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Erik</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Apr 10, 2020
at 12:55 PM Rebecca Kleemann <<a
href="mailto:rkleeman@students.uni-mainz.de"
target="_blank" moz-do-not-send="true">rkleeman@students.uni-mainz.de</a>>
wrote:<br>
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0px
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<div>
<p>Hi, <br>
</p>
<p>I want to add a group to set atoms to a constant
velocity.</p>
<blockquote>
<p><font size="-1" face="Courier New, Courier,
monospace">enum<br>
{<br>
egcTC, egcENER, egcACC, egcFREEZE,<br>
egcUser1, egcUser2, egcVCM,
egcCompressedX,<br>
egcORFIT, egcQMMM,<br>
egcNR<br>
};</font></p>
<p><font size="-1" face="Courier New, Courier,
monospace">const char *gtypes[egcNR+1] = {<br>
"T-Coupling", "Energy Mon.",
"Acceleration", "Freeze",<br>
"User1", "User2", "VCM", "Compressed X",
"Or. Res. Fit", "QMMM", nullptr<br>
};</font><br>
</p>
</blockquote>
<p>Are "User1" and "User2" meant to be used like
that and can they be renamed or should I add a new
group and increase the number of groups?</p>
<p>Greetings,</p>
<p>Rebecca<br>
</p>
</div>
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<div>Erik Lindahl <<a
href="mailto:erik.lindahl@dbb.su.se"
target="_blank" moz-do-not-send="true">erik.lindahl@dbb.su.se</a>></div>
<div>Professor of Biophysics, Dept.
Biochemistry & Biophysics, Stockholm
University</div>
<div>Science for Life Laboratory, Box
1031, 17121 Solna, Sweden</div>
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<div>Erik Lindahl <<a
href="mailto:erik.lindahl@dbb.su.se"
target="_blank" moz-do-not-send="true">erik.lindahl@dbb.su.se</a>></div>
<div>Professor of Biophysics, Dept. Biochemistry
& Biophysics, Stockholm University</div>
<div>Science for Life Laboratory, Box 1031, 17121
Solna, Sweden</div>
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