<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Berk,<br>
Thanks for the suggestion--I'll check if cut-offs are causing this
drift.<br>
<br>
--Mike Colvin<br>
<br>
<a class="moz-txt-link-abbreviated" href="mailto:hessb@mpip-mainz.mpg.de">hessb@mpip-mainz.mpg.de</a> wrote:
<blockquote
cite="mid:573b74ada2a1ff85168ed407deaea2cc.squirrel@squirrel.mpip-mainz.mpg.de"
type="cite">
<pre wrap="">Hi,
This sounds exactly like cut-off effects.
You have to be very careful with several mdp options
to get good energy conservation.
If you want this or not depends on your goals.
For good energy conservation you have to use, for instance,
vdwtype=shift with a buffer region and coulombtype=pme.
Berk
</pre>
<blockquote type="cite">
<pre wrap="">Hi Mark,
Thanks for that pointer. I'm using Gromacs 4.0.3 and the drifting
"Conserved En" value seems to occur in any NVT simulation using the
Bussi, et al. thermostat. To give a specific example, if one starts
with the water example in the Gromacs distribution
(gromacs-4.0.3/share/tutor/water) and changes the thermostat to
"v-rescale", turns off the barostat, and comments out an obsolete
option, and then runs it ("grompp" and "mdrun"), the resulting energy
file will show a linearly increasing "Conserved En". Here's the diff
file between the new and original mdp files:
31c31
< ;bd-temp = 300
---
> bd-temp = 300
123c123
< Tcoupl = v-rescale
---
> Tcoupl = berendsen
130c130
< Pcoupl =
---
> Pcoupl = berendsen
Thanks in advance for any guidance on this.
--Mike Colvin
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Hi All,
First, thanks to the developers for quickly incorporating Bussi,
et al.'s new velocity rescaling thermostat. The thermostat works
great, but I have a question about the "Conserved En" term reported,
which so far as I could glean from the source is the same as the
Bussi's effective energy (H hat) defined in eq. 15 of his paper.
However, for some NVT test simulations that seem otherwise very well
behaved, the Conserved Energy changes steadily over the simulation
which I wouldn't expect for simulations with sufficiently small time
steps. For a liquid argon test case (T=303.9, dens=1.485 gm/cm3) this
value drops exactly linearly in time with a slope that is exactly
proportional to the timestep (tested at 2fs, 1fs, and .5 fs). For an
SPC/E water (at STP) this value drifts upward during the simulation
with a slope that is roughly proportional to the square root of the
timestep (ts=.25, .5, 1, and 2fs). Anyway, I was curious if anyone
else had noticed this phenomena and whether I'm misinterpreting what
this term is. (And please let me know whether this or the gmx-user
list is the best place for a question like this.)
</pre>
</blockquote>
<pre wrap="">I can't help you on the point of your question, but if there's a real
issue involved, at the very least people will want to know your
GROMACS version, the contents of your .mdp file and mdrun command
line. You may get a helpful response more quickly if you provide that
information.
Mark
_______________________________________________
gmx-developers mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-developers">http://www.gromacs.org/mailman/listinfo/gmx-developers</a>
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.
</pre>
</blockquote>
<pre wrap="">_______________________________________________
gmx-developers mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-developers">http://www.gromacs.org/mailman/listinfo/gmx-developers</a>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.
</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
</body>
</html>