I did not try addIons2. "addIons2" is too slow for a big water box.
Also, it treats solvent the same as solute. I think it will end with
ions out of solvent.
Wei
On Fri, Jul 22, 2011 at 5:37 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
> Does the use of *addIons2* in place of *addIons *not solve the issue?
>
> Hirdesh
>
> On Fri, Jul 22, 2011 at 6:00 PM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Thu, Jul 21, 2011, Wei Chen wrote:
>> >
>> > After I solvated my protein, I used "addIons" to add ions to the
>> > system to reach certain ion concentration. I found that some ions were
>> > placed outside of the water box. Is this normal? When I used AMBER8
>> > long time ago, this did not happen. I was wondering if this is
>> > something with the new version of AmberTools.
>>
>> It's been seen before I think: http://archive.ambermd.org/201007/0205.html
>>
>> (Just use the search box on the Amber mailing list web page). But I don't
>> know that it was ever resolved, so if Dan is willing to look at it, that is
>> fine. Presumably, (a) most people never study the distribution of ions too
>> closely, and/or (b) equilibration makes the simulation forget about the
>> details of the intial condition anyway.
>>
>> ....dac
>>
>>
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Received on Fri Jul 22 2011 - 11:30:02 PDT
