Hi Chris,<br><br>thanks for the question.<br><br>This made me realize that I changed the default behavoir more than makes sense at this moment. <br><br>I don't think it is a good idea to not append the default filetype to output files. And even for input files it is in general not good. Because the filetype is based on the ending. And for non-trajectory input it has to be one of the GROMACS types. <br>
<br>So I reverted the default behavior unless for reading of trajectory data. Because there it makes sense and also has no weird side effects.<br><br>For your problem:<br>There is a noconfout option to mdrun. May be we should add also a -nolog option and don't create the trajectory or energy file if anything is written (if nstenergy/nstxout is 0).<br>
<br>Roland<br><br><div class="gmail_quote">
On Thu, Nov 26, 2009 at 9:07 AM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</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;">
Hi Roland,<br>
<br>
You mention that now "The default extension is only added if the specified file does not exist." Does this mean that I can now do this:<br>
<br>
mdrun -deffnm this -o /dev/null -c /dev/null -g /dev/null<br>
<br>
This would be very convenient to alleviate demand on our file system where we are running very many very short simulations and the opening/closing is beginning to cause problems.<br>
<br>
Thanks,<br>
Chris.<div><div></div><div><br>
<br>
Quoting Roland Schulz <<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>>:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
I just commited the Gromacs support for the VMD molfile plugin API.<br>
<br>
This allows all analysis tools to read all VMD supported trajectory formats<br>
(e.g. DCD).<br>
It requires a VMD binary compiled with the same architecture as GROMACS<br>
(e.g. both 64bit).<br>
It is by default compiled in in case dlopen is supported (thus for all mayor<br>
architectures).<br>
<br>
It changes one earlier behavior (even if dlopen support is not compiled in):<br>
The default extension is only added if the specified file does not exist.<br>
e.g. if both the file file.dcd and test.dcd.xtc exist then g_rms -f test.dcd<br>
reads file.dcd and not test.dcd.xtc.<br>
<br>
Roland<br>
<br>
--<br>
ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>
865-241-1537, ORNL PO BOX 2008 MS6309<br>
<br>
</blockquote>
<br>
<br>
<br></div></div><font color="#888888">
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</font></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>