[gmx-users] Energy Minimization

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 10 13:06:24 CET 2012

On 10/01/2012 10:46 PM, Steven Neumann wrote:
> Thank you. Imagine I would like to put ligands in further simulations. 
> Should I then copy coordinates of my ligands in smaller box (not to 
> overlap my tube) and then copy both coordinates of ions and ligands 
> plus protein?

Any way you want to construct your non-overlapping non-solvent non-ion 
molecules is fine. Previous EM of each is wise, but not necessarily 
required - vacuo EM is probably fine. Then solvate, then use genion, 
then EM the whole system. Copying ions from earlier calculations is a 
good way to generate atomic clashes, which is a high price to pay for 
randomly-placed ions that are different from those generated as above.


> On Tue, Jan 10, 2012 at 11:31 AM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 10/01/2012 10:13 PM, Steven Neumann wrote:
>         Thank you. Should I also copy and paste coordinates of my ions
>         or just my protein?
>     The randomly-placed ions will be immaterial for EM.
>     Mark
>     -- 
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