From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Thu Oct 15 2015 - 21:50:20 CDT
I am trying to move part of a protein with constant velocity. I have found
two options (from the manual and tutorial) - SMD and moving constraints. In
fact, I have already tried both and found "moving constraints" is more
suitable for my case as the protein is quite flexible while I would like to
have the minimum structural deformation. My questions are as follows:
1. What is meant by "moving the center of mass" indicated by SMD options
and how in exact does it add forces to each atom during simulation? "moving
constraints" is relatively more straight forward for me as it adds
constraints individually to each atom I specified.
2. While SMD has the function to output related forces, positions, etc.,
how can I get forces added by the constraint function separately in the log
Any response is appreciated. Thanks in advance.
City University of Hong Kong
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