We might more data or even look at your code, but for starters, VMD
starts counting atoms from 0 and amber from 1. Maybe you already
corrected for this, but it is something that happens quite a bit.
Adrian
On 5/13/20 7:32 PM, Amanda Buyan wrote:
> [External Email]
>
> 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_file
> &colvar
> 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
>
> Amanda
>
>
>
> Dr. Amanda Buyan
>
> Postdoctoral Fellow, Corry Lab
>
> Research School of Biology
>
> 134 Linnaeus Way
>
> Canberra, ACT 2601
>
> amanda.buyan.anu.edu.au
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed May 13 2020 - 17:00:02 PDT
