[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.
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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