if you have ions in your system, and you are using 2 groups, try define them as protein & non-protein.<br>
<br>
Don't modify the source without knowing what u are doing. Gromacs can
handle your groups... Take some time to read the manuals...<br><br><div><span class="gmail_quote">On 2/14/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Tamas Horvath wrote:<br>> Check out what groups you have. The values at tau_t and ref_t refer to
<br>> those groups.<br>> In the default case, in the demo, those refer to "protein" and "SOL"<br>> groups.<br><br>Indeed, there are probably ions in the pdb file.<br><br>><br>> On 2/14/06, *David Mathog* <
<a href="mailto:mathog@caltech.edu">mathog@caltech.edu</a><br>> <mailto:<a href="mailto:mathog@caltech.edu">mathog@caltech.edu</a>>> wrote:<br>><br>> I'm still struggling with gromacs. The gmxdemo script runs.
<br>> So I tried to scale up a bit and chose more or less at random a<br>> protein with some CYS-CYS bonds (H2MCM.PDB) and tried to plug it<br>> into the gmxdemo script instead of "cpeptide".
<br>><br>> No Joy.<br>><br>> It eventually comes completely off the rails at the grompp pr section<br>> where it comes up with this gem:<br>><br>> Fatal error:<br>> Not enough ref_t and tau_t values!
<br>><br>> pr.mdp has these lines:<br>><br>> tau_t = 0.1 0.1<br>> ref_t = 300 300<br>><br>> which are straight from the gmxdemo script.<br>><br>> The
3.2 manual has no matches on "tau_t" or "ref_t".<br>><br>> It looks like the programs wants more columns on these lines, but<br>> how many, and why that many???<br>><br>> Thanks,
<br>><br>><br>> David Mathog<br>> <a href="mailto:mathog@caltech.edu">mathog@caltech.edu</a> <mailto:<a href="mailto:mathog@caltech.edu">mathog@caltech.edu</a>><br>> Manager, Sequence Analysis Facility, Biology Division, Caltech
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</a><br><br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
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