<p dir="ltr">-rmpbc (and -pbc) can be controlled with flags set in TrajectoryAnalysisSettings. For the selection options, you will need to change the framework code (e.g., such that if the tool does not provide any selection options, then those common options are also omitted). Since all existing tools use selections, this hasn't been a consideration earlier.</p>
<p dir="ltr">Teemu</p>
<br><div class="gmail_quote"><div dir="ltr">On Tue, Nov 10, 2015, 13:40 David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
(how) can I get rid of the following default options in my tool?<br>
<br>
-[no]rmpbc (yes)<br>
-sf <file><br>
-selrpos <enum> (atom)<br>
<br>
Cheers,<br>
--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" rel="noreferrer" target="_blank">http://folding.bmc.uu.se</a><br>
--<br>
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