<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><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><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 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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