Dear Carlos,
Thanks a lot for your explanation! I am still a little confused here.
Since 0 padding was added by solvatebox, I am not sure how the total vdw
box size
is being different from the solute box dimension.
Then, how should I get a exact box size what I want, trial and editing
the coordinates file? Thanks a lot!
All the best,
Qinghua
On 06/01/2018 07:59 PM, Carlos Simmerling wrote:
> the solvatebox command will build a box using your solute coordinates, and
> adding 0 padding (the final value on the solvatebox line) beyond the
> solute. So your solute dimensions are defining your box coordinates.
>
> On Fri, Jun 1, 2018 at 1:10 PM, Qinghua Liao <scorpio.liao.gmail.com> wrote:
>
>> Hello everyone,
>>
>> I am trying to set the water box size, but I failed to get what I want.
>>
>> For example, I tried to put the protein in a water box with commands:
>>
>> set mol box {160 160 160}
>> solvatebox mol TIP3PBOX 0.0
>>
>> Then the box information I got is something like this:
>>
>> Solute vdw bounding box: 160.000 160.000 160.000
>> Total bounding box for atom centers: 160.000 160.000 160.000
>> Solvent unit box: 18.774 18.774 18.774
>> Total vdw box size: 175.760 163.366 162.873 angstroms.
>> Volume: 4676619.621 A^3
>>
>> The box size is 175.760*163.366*162.873 A3, but not 160.0*160.0*160.0 A3
>> which is what I expected.
>> Could someone tell me how and why the new box size was generated? Thanks
>> a lot!
>>
>>
>> All the best,
>> Qinghua
>>
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Received on Fri Jun 01 2018 - 11:30:02 PDT
