[gmx-users] big protein dynamics
adriana at ms.fci.unibo.it
Wed Nov 30 17:45:31 CET 2005
On Wed, 30 Nov 2005, Tsjerk Wassenaar wrote:
> Hi Adriana,
> Did you energy minimize your system before this?
> A pretty robust regime to follow is:
> 1. energy minimize in vacuum
> 2. energy minimize after solvation
> 3. perform position restrained MD
> 4. run a short simulation with temperature coupling to equilibrate
> 5. turn on pressure coupling and let the system equilibrate
> 6. harvest
Yes, it's a structure just minimize...
maybe the position of some water molecules are within the protein
I try to minimize the box with both protein and water...
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