Re: Colvar vs. SMD

From: Giacomo Fiorin (
Date: Wed Mar 16 2022 - 10:22:06 CDT

Hi Steve, I was about to send this reply before seeing Jérôme's. The
configuration is truncated, and I don't see in particular the part where
the restraint center is moved. You should have "target*" options in the
harmonic restraint config, as shown in this example:*sec:colvars_crash_course__;Iw!!DZ3fjg!uevFQk1KZgzAwvjrItaW5uK9soc1rPU04OOKytmp1ayNO61JTN0y0Jy8tBAaVNRkCQ$

You could also enable outputCenters and outputAccumulatedWork
<*sec:colvarbias_smd__;Iw!!DZ3fjg!uevFQk1KZgzAwvjrItaW5uK9soc1rPU04OOKytmp1ayNO61JTN0y0Jy8tBDHisCbdw$ >
to get a rough "PMF" (note the quotes: it's still SMD!), to process via
your own plotting tools or this convenience script
<;!!DZ3fjg!uevFQk1KZgzAwvjrItaW5uK9soc1rPU04OOKytmp1ayNO61JTN0y0Jy8tBAZoETPMw$ >

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