Thanks Dac for your reply. I will take care of proper equilibration before
proceeding to production. Will also try with randomizeions command. this
seems a good option to modify the starting structure.
Thanks for your support.
Hirdesh
On Tue, Feb 7, 2012 at 6:23 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Feb 07, 2012, Hirdesh Kumar wrote:
>
> > I am trying to prepare my protein in tleap. I loaded the protein,
> solvated
> > it with TIP3PBOX water type and now I am trying to neutralize the charge
> > with Na+ counter ions. But the added charges are in close vicinity of the
> > protein structure and I am afraid that it may affect simulation. I am
> using
> > following command for adding counter ions
> > *addIons var Na+ 0*
>
> This should work, and is what is commonly done. Don't forget that you need
> lots of equilibration of the solvent before proceeding with a "production"
> calculation to be analzyed. The purpose of the equilibration is to reduce
> the
> dependence on details of the starting structure.
>
> You might also look at the "randomizeions" command in ptraj.
>
> ....dac
>
>
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Received on Tue Feb 07 2012 - 05:00:04 PST
