This didn't seem to solve the problem, so I've submitted a bugzilla. I
can, of course, run the constant pressure equilibration with position
restraints rather than freeze groups if necessary, but I would rather
use freeze groups for everything if possible, since I really don't want
the protein to move at all, ever, in what I'm doing. I just want to
equilibrate at constant pressure to bring the bath to the right
pressure.<br>
<br>
Thanks,<br>
David<br><br><div><span class="gmail_quote">On 1/4/06, <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;">
David Mobley wrote:<br>> Dear all,<br>><br>> I've just started trying to use freezegroups to freeze a protein I've<br>> been running MD on. As far as I can tell, according to the manual,<br>> freezegroups = Protein should work even with pressure coupling
<br>> (Berendsen); the frozen groups should just be left unscaled by the<br>> thermostat. Therefore, I thought it would at least be worth trying<br>> having my protein frozen during constant pressure equilibration with
<br>> Berendsen.<br>><br>> However, my log file (whenever I have pressure regulation) rapidly fills<br>> up with the following:<br>><br>> Correcting invalid box:<br>> old box (3x3):<br>> old box[ 0]={-
9.99426e+21, 0.00000e+00, -0.00000e+00}<br>> old box[ 1]={ 0.00000e+00, -9.99426e+21, -0.00000e+00}<br>> old box[ 2]={-4.99713e+21, 3.07191e+28, -7.06701e+21}<br>> new box (3x3):<br>> new box[ 0]={-
9.99426e+21, 0.00000e+00, -0.00000e+00}<br>> new box[ 1]={ 0.00000e+00, -9.99426e+21, -0.00000e+00}<br>> new box[ 2]={-4.99713e+21, 3.07191e+28, -7.06701e+21}<br>><br>> The log file quickly runs away to several GB and I killed the job to
<br>> prevent overfilling my disk. Does this mean that freeze groups actually<br>> do *not* work properly with pressure control? Or have I done something<br>> wrong? I can submit a bugzilla if necessary.<br>If you have tried weaker coupling (
e.g. tau_p = 2 ps) and it still<br>happens then please do file a bugzilla.<br><br>><br>> Thanks,<br>> David<br>><br>><br>> ------------------------------------------------------------------------<br>>
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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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