There were no groups specified in the neutralize.mdp file. I specified the solvent and DNA and it worked.<br><br>Thanks.<br><br><div class="gmail_quote">On Sun, Sep 20, 2009 at 2:32 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
Gunnar Widtfeldt Reginsson wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi. I am new to Gromacs and I am following the tutorial on <a href="http://wwwuser.gwdg.de/%7Eggroenh/SaoCarlos2008/html/build.html#top" target="_blank">http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top</a><br>
<br>
I have managed to get the DNA into a water box. When I run genbox I use the ffamber_tip4p.gro water model.<br>
When I then run:<br>
grompp -f neutralize.mdp -c solved.pdb -p topol I get this fatal error:<br>
where neutralize.mdp is from the website above.<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 4.0.5<br>
Source code file: readir.c, line: 1463<br>
<br>
Fatal error:<br>
Invalid T coupling input: 0 groups, 2 ref_t values and 2 tau_t values<br>
-------------------------------------------------------<br>
<br>
<br>
I have been searching for an explanation to this error but haven't found anything. Can somone please help. <br>
</blockquote>
<br></div></div>
Not without seeing the relevant section of your .mdp file, but it looks like you haven't actually specified any groups to be subject to temperature coupling.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks.<br>
<br>
<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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