"addIons" does not behave like this (ions out of solvent) for tleap in
AMBER8 in my experience. Probably, some codes were changed in
AmberTools.
Wei
On Fri, Jul 22, 2011 at 11:25 AM, Wei Chen <cwbluesky.gmail.com> wrote:
> 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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>>>
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Received on Fri Jul 22 2011 - 11:30:03 PDT
