restraining bonds

From: Neelanjana Sengupta (
Date: Sun Aug 31 2014 - 23:50:24 CDT

Dear NAMD community,

I need to do a protein simulation, wherein all individual bonds between the
non-hydrogen atoms are harmonically restrained. (I do not wish to restrict
the overall translation of the protein). Since there are many such bonds,
the colvar option "distance" (with group1 and group2) may not work.

Any suggestions on how to go about this?

Thanks in advance.


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