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David van der Spoel wrote:<br>
<blockquote type="cite" cite="mid:Pine.LNX.4.10.10207252050320.25400-100000@zorn.bmc.uu.se">
<pre wrap="">On Thu, 25 Jul 2002, alexander yakovenko wrote:<br><br></pre>
<blockquote type="cite">
<pre wrap="">Dear all,<br>I work with nonproteion molecules using gromacs, and have some problems.<br>Does anybody know is the gromacs MD simulation crash if the number of<br>charge groups in rtp file more than 32 ? I have about ten examples of<br>such crashing, but it may be the problem of my molecules type. This crush<br>took place in MD simulation only, but not in energy minimization.<br></pre>
</blockquote>
<pre wrap=""><!---->Charge groups can not be larger than 32 atoms (we use an integer as<br>bitmask somewhere). If you use PME you can certainly make your charge<br>groups smaller, it wil lnot affect the coulomb interactions.</pre>
</blockquote>
Just to clarify; there is a very good reason why you shouldn't ever consider
charge groups of size>32<br>
(otherwise we would of course fix that limitation). Charge groups are used
in the neighborsearching too<br>
speed things up, so if you have two huge chargegroups some of the atoms may
be very close even if the<br>
centers-of-mass of the charge groups are not. If the centers are further
apart than the cut-off, you will<br>
still not get any interaction at all between the atoms close to each other!.
<br>
<br>
Since a cut-off is typically in the order of 1nm, even the best case of perfectly
spherical charge groups<br>
could lead to severe errors if you have as much as 32 atoms in them.<br>
<br>
Cheers,<br>
<br>
Erik<br>
<br>
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