<br><br><div class="gmail_quote">On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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 class="im"><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
I am trying to do a calculation on an artificial line charge in vacuum. The line charge has 267 atoms and each atom has a 1e charge. The atoms are bonded by a bond term and an angle term. I defined the required itp <br>
</blockquote>
<br></div>
If you're trying to keep the atoms in a line, the system will not be stable. Angles of 180 degrees routinely crash.</blockquote><div><br></div><div>Not even if i use a 3 body angle term with equilibrium angle = 180? If not then why ?</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
files and top file. When i issue<br>
<br>
grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp<br>
<br>
I get the following error message.<br>
<br>
Program grompp_jpt, VERSION 4.5.3<br>
Source code file: grompp.c, line: 175<br>
<br>
Fatal error:<br>
The largest charge group contains 267 atoms. The maximum is 32.<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors</a><br>
<br>
What should i try to do to circumvent this error.<br>
<br>
</blockquote>
<br></div>
The maximum charge group size is defined in the include/types/nblist.h header. You can alter the value there, which will get around the error, but consider whether or not this is even a good physical model. If all atoms are in the same charge group, there are no electrostatic interactions between these atoms since neighbor searching is done and short-range energies are calculated based on inter-charge group distances. I have no idea how to properly simulate a line of positively-charged particles, but be aware.<br>
</blockquote><div><br></div><div>Thanks for the pointer and the awareness remark. But since this is a model system and for the physical problem i am trying to deal with its alright if the atoms within the line charge do not interact via non-bonded potentials.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
-Justin<br>
<br>
-- <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><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></blockquote></div><br>