Justin, when i define the whole line charge as a charge group i do get a coulomb energy contribution. I thought there would be no non-bonded contribution. I use a very high cut-off (longer than chain length) and no pbc. Am i missing something ?<br>
<br><div class="gmail_quote">On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey <span dir="ltr"><<a href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I was not sure if changing the size of maxcg would not negatively influence anything else. I will give it a try. Thanks Justin<div><div></div><div class="h5"><br><br><div class="gmail_quote">On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I change the maximum charge group size defined in the include/types/nblist.h header from 32 to 267. Then grompp worked fine but the mdrun did not start. The following error came out<br>
<br>
Program mdrun_jptlc, VERSION 4.5.3<br>
Source code file: ns.c, line: 2417<br>
<br>
Fatal error:<br>
Max #atoms in a charge group: 267 > 64<br>
<br>
</blockquote>
<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
/* Verify whether largest charge group is <= max cg.*<br>
* This is determined by the type of the local exclusion type *<br>
* Exclusions are stored in bits. (If the type is not large*<br>
* enough, enlarge it, unsigned char -> unsigned short -> unsigned long)*<br></div>
*/<br>
</blockquote>
<br>
The solution is described in the comment above.<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
maxcg = sizeof(t_excl)*8;<br>
</blockquote>
<br></div>
Increase the size here.<br><font color="#888888">
<br>
-Justin</font><div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
if (nr_in_cg > maxcg)<br>
{<br>
gmx_fatal(FARGS,"Max #atoms in a charge group: %d > %d\n",<br>
nr_in_cg,maxcg);<br>
}<br>
</blockquote>
<br></div><div><div></div><div>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
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