[gmx-users] constrain h-bonds

[Nguyen Hoang Phuong]

> On Thu, 2002-12-05 at 16:04, Nguyen Hoang Phuong wrote:
> > 
> > Dear All,
> > 
> > I would like to do simulation for the system consisting a peptide in
> > flexible waters. I would like to constrain the h-bonds of the peptide but
> > not for waters. Does anyone know how to do that? Thanks in advance.
> It's not so simple, you have to define constraints rather than bonds for
> the h-atom bonds in the protein (or modify the code that does the bond
> to constraint conversion in grompp to do it differently per molecule)
> 
> -- 

I define the distance restraint for the N-H bond in the peptide:

[distance_restraints]
; ai    aj     type    index  type'     low      up1    up2    fac
  4      5      1       0       1       0.1   0.104   0.104   100.0

and in the *mdp file the value disre_fc = 20000. However, the distance N-H
still fluctuates between (0.09,1.080) during simulations. If I increase
the force then the simulations is died! Any suggestions? Thanks in 
advance.

Phuong

> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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