This could be a visualization problem with vmd. Have you done a hard check
? I.e., check whether the difference in max and min of coordinates is less
than the box dim ?
On Mon, 12 Jan 2026, 07:23 Arun Srikanth, <askforarun.gmail.com> wrote:
> How are you visulizing the box, i mean what software ?
>
> Arun
>
> On Mon, 12 Jan 2026, 07:02 Sree Gouri Menon via AMBER, <amber.ambermd.org>
> wrote:
>
>> Dear AMBER users,
>>
>> I am encountering an issue with solvation box generation in tleap and
>> would
>> appreciate some guidance.
>>
>> I am studying aggregation and have placed 10 copies of my molecule in a
>> box
>> to create the initial configuration. After loading this system into tleap
>> and adding water and ions, the solvation box generated by tleap does not
>> fully enclose all 10 molecules. In particular, 1–2 molecules extend
>> outside
>> the box boundaries, and the box itself appears poorly positioned relative
>> to the solute.
>>
>> I have tried increasing the solvation box size (using larger buffer
>> distances / box dimensions), but the problem persists — the box still does
>> not accommodate all molecules. This is confusing because the original
>> structures were generated inside a cubic box of ~15 nm per side, and the
>> solvation box dimensions I specify in tleap are larger than this. I have
>> attached an image showing the issue for clarity.
>>
>> Is there a recommended workflow to ensure that all molecules are properly
>> enclosed before solvation (e.g., recentering, resetting the unit cell, or
>> specific tleap commands)?
>>
>> Any suggestions or pointers would be greatly appreciated.
>>
>> Thank you for your time and help.
>>
>> Best regards,
>> Sree Gouri
>> [image: image.png]
>>
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Received on Mon Jan 12 2026 - 01:30:20 PST
