[gmx-users] bond deviation

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 10 20:59:56 CET 2002

On Thu, 10 Jan 2002, sadhna wrote:

>    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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