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<div class="moz-cite-prefix">Which paper are you referring to? And
what do you mean with current v?<br>
In any algorithm, you should scale the velocity at the exact same
time you computed the kinetic energy for. That is what the code
since 4.6 does, right?<br>
But note that as tau is usually much larger than dt, the
difference will be extremely small. But the v-rescale thermostat
is implemented such that one can use tau=dt, or even tau=0, and
get a fully correct ensemble.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2017-06-09 15:10, Zachmann, Martin wrote:<br>
</div>
<blockquote cite="mid:8864d1052cb24e90ae34338374586882@tum.de"
type="cite">
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<p>Thank you so much for your fast answers.</p>
So you are saying the difference from the code to the original
paper (as is now also the case in the current master-branch<br>
in <span class="pl-en">updateMdLeapfrogSimple</span>()) is on
purpose?<br>
It says in the paper that scaling the current v with a lambda
calculated from minus half-step v is incorrect, yet<br>
acceptable since lambda changes slowly.<br>
regards Martin<br>
</div>
<br>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>
<a class="moz-txt-link-rfc2396E" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><gromacs.org_gmx-developers-bounces@maillist.sys.kth.se></a>
on behalf of Berk Hess <a class="moz-txt-link-rfc2396E" href="mailto:hess@kth.se"><hess@kth.se></a><br>
<b>Sent:</b> Friday, June 9, 2017 2:51:46 PM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
<b>Subject:</b> Re: [gmx-developers] do_update_md</font>
<div> </div>
</div>
<div>
<div class="moz-cite-prefix">On 2017-06-09 14:29, Mark Abraham
wrote:<br>
</div>
<blockquote
cite="mid:CAMNuMARaO76EAqD7Jf=30stA4thSdfCAj+Tebhgofn5nriTj4A@mail.gmail.com"
type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>That looks like a bug that was silently fixed during
the adoption of the velocity-rescale thermostat of Bussi
(see commit 333641e040ae824badf9d9531290a46ad581ed53). It
may be that the issue wasn't noticed because people often
used parameters that produce lg == 1...</div>
</div>
</blockquote>
Is debatable if one should call that a bug. The original
Berendsen thermostat that this code was written for did not
produce the correct ensemble anyhow, so it was likely purposely
coded this way to give better/more scaling with consistently too
high temperature, as would happen with the group cut-off scheme
and no pair list buffering. With the V-rescale thermostat you
should scale the velocity you computed the temperature for,
which are the minus half-step velocities, as is now correctly
done.<br>
In practice it will be difficult to detect a difference between
these two codes.<br>
<blockquote
cite="mid:CAMNuMARaO76EAqD7Jf=30stA4thSdfCAj+Tebhgofn5nriTj4A@mail.gmail.com"
type="cite">
<div dir="ltr">
<div><br>
</div>
<div>I would strongly advise avoiding doing development work
on unsupported versions of the software more than five
years old... ;-) Get the git master branch and stay up to
date with the hundreds of bugs that have been fixed since
:-)</div>
</div>
</blockquote>
His mail didn't imply he is using an old version for
development, it could just be for trying to understand the code
or porting changes from an old version to master, which is good!<br>
<br>
Cheers,<br>
<br>
Berk<br>
<blockquote
cite="mid:CAMNuMARaO76EAqD7Jf=30stA4thSdfCAj+Tebhgofn5nriTj4A@mail.gmail.com"
type="cite">
<div dir="ltr">
<div><br>
</div>
<div>Mark</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Fri, Jun 9, 2017 at 2:01 PM Zachmann,
Martin <<a moz-do-not-send="true"
href="mailto:m.zachmann@tum.de">m.zachmann@tum.de</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div id="m_829167863962055915divtagdefaultwrapper"
style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif"
dir="ltr">
<p>Hello community!</p>
<p>i hope someone can help me understand some code
changes in the do_update_md() function in
update.cpp.</p>
<p>In the case where it advances r and v in the
leap-frog scheme together with the berendsen
thermostat<br>
</p>
<p>(last two else if { } and else { }) in version
4.0.7. it looks like this</p>
<p><span>vv = lg*(vn + f[n][d]*w_dt);<br>
</span></p>
<p><span>where lg is the lambda-scaling factor from
the thermostat and w_dt is dt/m.</span></p>
<p><span>Instead in version 4.5. and higher:</span></p>
<p><span></span><span> vv = lg*vn + f[n][d]*w_dt;</span></p>
<p><span><br>
</span></p>
<p><span>The original paper (<span>The Journal of
Chemical Physics 81, 3684 (1984); doi:
10.1063/1.448118</span>) seems to scale</span></p>
<p><span>both old velocity and force. Btw in <span>do_update_visc</span>()
scaling is done to both.</span></p>
<p><span>What is the purpose of this?</span></p>
<p><span>any help is much appreciated,</span></p>
<p><span>regards Martin<br>
</span></p>
<p><br>
</p>
</div>
</div>
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