HI all
This is an SMD file to be used with jar=1 for SMD runs
It sets up two groups, each described as the center of mass of the atoms
listed in the file.
Should be easy to modify for your own purposes.
Adrian
On 1/3/12 8:20 PM, pxc.cqu.edu.cn wrote:
> Hello amber users,
> Happy new year!
>
> I'm trying to simulate the process of membrane protein transferring peptide, and I repeated the example following the amber tutorial. But I don't kown how to set the dist.RST file in my simulation. I think the peptide should be taken as a whole, the distance between CA in the backbone of membrane protein and the center of mass of peptide should be changed. So how to set r2, rk2, r2a, igr1, igr2, grnam2, and grnam2(2) and what the meaning of igr1, igr2, grnam2, and grnam2(2)? I have read the tutorial, but I can't fully understand. Could you give me some advice? Thanks.
>
> Best regards,
>
> Xc PAN
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--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Tue Jan 03 2012 - 18:00:02 PST
