<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">hess@kth.se</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<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">rkleeman@students.uni-mainz.de</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<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">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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