[AMBER] Steered MD with COM_ANGLE

From: Amanda Buyan <Amanda.Buyan.anu.edu.au>
Date: Wed, 13 May 2020 23:32:22 +0000

Hi everyone,

I am trying to do a Steered MD simulation, where I am calculating the centre of mass of an angle between three atom groups. I've already checked in VMD to see that the indices I am using for the atoms are correct. When I run with the following input file, I don't get any movement of the collective variable:

cv_type = 'COM_ANGLE'
cv_ni = 14,
!          |    one vertex                                     |    middle                |          second vertex                          |
cv_i = 51401,51415,51421,51436,51446,0,5118,0137,5153,0,6215,6236,6246,7999,8015,8031,0,
nharm = 1,
harm = 30.0,
npath = 2,
path = 20.0,120.0,
path_mode = 'LINES',
do I have everything correct (I don't normally have the comment in there - I put it in for easy reference?  Could it be something as simple as wrong atom selections, even though I've checked those twice?  The Amber manual is also not clear about the ordering of the three atom groups, so I'm unsure if I have that right...
Best wishes
Dr. Amanda Buyan
Postdoctoral Fellow, Corry Lab
Research School of Biology
134 Linnaeus Way
Canberra, ACT 2601
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Received on Wed May 13 2020 - 17:00:02 PDT
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