[gmx-users] bond deviation

[David van der Spoel]

On Thu, 10 Jan 2002, sadhna wrote:

>
>hi,
>    I am trying to simulate protein in water for 1ns. I want to
>equilibrate solvent before simulation because the protein is not
>maintaining the desired structure due to large solvent forces.
>I tried doing it by giving following in mdp file for em in water:
>freezegrps           = protein SOL
>freezedim            = Y Y Y N N N
> 
>but after starting mdrun for 1ns i am geeting fatal error;Bond deviates
>more than half its own length

Do you run freeze for 1 ns to equilibrate? That sounds excessive.
You have to turn off pressure coupling and to define center-of-mass groups
protein and SOL. I assume the LINCS error in the protein. Anything else
special? Timestep etc.

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://zorn.bmc.uu.se/~spoel
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