[gmx-users] harmonic potential on the distance between two atoms

Yang Ye leafyoung81-group at yahoo.com
Wed Feb 15 01:35:34 CET 2006


3A could be too small for the inter-atomic distance. Could you check again?
To bind two atoms, I suggest to use distance_restraints. It could impose no
penalty to atoms when they are within permissible range.

Yang Ye
Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Tel: 65 6316 2884

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of wang xiaoling
> Sent: Wednesday, February 15, 2006 5:53 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] harmonic potential on the distance between two atoms
> Hi,
> I am doing simulation on a single peptide (352 atoms)
> solvated in a box of water. I want to apply a harmonic
> interaction between two atoms on the peptide which are
> not chemically bonded. So I add a section in the top
> file:
> [ bonds]
> ;  ai    aj funct      b0           kb
>     1   349     6      3.0e-01      1.0e+01
> My mdrun stopped right after started, leaving quite a
> few step??.pdb files. The MD log file say:
> There were 2 inconsistent shifts. Check your topology.
> If I don't include the above section in the top file,
> it runs perfectly. I have also tried to vary the value
> of b0 and kb, still failed.
> Could someone tell me what is wrong with my way of
> implementing harmonic potential?
> Thanks.
> Shirley
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