Actually, it doesn't really matter what you do first and do the other next
if the role of the ion is simply a part of solvent. But, I prefer to add
ions first. If you add ions first, your ions will be located closer to your
solute. If you add ions after adding water molecules, your ions will be
mostly placed near the boundary of the periodic box. In any case, after you
let the system relax in NTP for a while, the both approaches shouldn't make
any difference.
You can also 'randomizeion' using ptraj after you build the topology file.
Then, the ions will be randomly scattered all over the solvent. However,
you should be careful using this command if there is any bridging ions or
any structural ions.
On Sat, Mar 13, 2010 at 5:51 AM, Nicee <nicee.srivastava.imtech.res.in>wrote:
> Hello all,
>
> I am little confused as whether I should addions first and then solvate the
> system or solvate first and then addions. which approach is better. kindly
> clear
> the confusion.
>
> Thanks.
>
> Nicee
>
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--
Best,
InSuk Joung
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Received on Sat Mar 13 2010 - 09:00:02 PST
