Thanks Justin, I can see that there is no problem when i fix the periodicity.<div><br></div><div>Amit<br><div><br><div class="gmail_quote">On Tue, Jul 19, 2011 at 2:52 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><div></div><div class="h5"><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 doing dppc-water simulation. I am using structure and topologies from <br>
<a href="http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies" target="_blank">http://moose.bio.ucalgary.ca/<u></u>index.php?page=Structures_and_<u></u>Topologies</a><br>
<br>
In version 4.0 when i do grompp_v4.0.2 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top<br>
<br>
it creates npt.tpr without any errors.<br>
<br>
Using the same structure and topologies when i issue<br>
<br>
grompp_v4.5.3 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top<br>
<br>
it gives out the following warning<br>
<br>
Largest charge group radii for Van der Waals: 5.354, 5.297 nm<br>
Largest charge group radii for Coulomb: 5.354, 5.297 nm<br>
WARNING 1 [file npt.mdp]:<br>
The sum of the two largest charge group radii (10.650990) is larger than<br>
rlist (1.200000)<br>
<br>
I dont think the charge group should be so big. Can someone suggest what is going on ?<br>
<br>
</blockquote>
<br></div></div>
The input file contains broken molecules. There is nothing wrong, per se, but only in the case when molecules are split across periodic boundaries. This is a new check as of version 4.5.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Ami<br>
<br>
</blockquote>
<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>
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