Sorry, I think I do not fully get your idea.
I just load the .prmtop and the output .nc file into VMD and see the system expanding without boundary limit. I suppose the system should likely maintain in a periodic box and form a cube like structure as shown in the tutorial website.
At 2021-09-08 19:49:53, "David A Case" <dacase1.gmail.com> wrote:
>On Wed, Sep 08, 2021, wangwei1669 wrote:
>
>>For both situation the density and volume in the output file are maintaing
>>stable during the simulation. And they do not change a lot near where it
>>crashes for situation 1. However, the values are also strange since the
>>system in fact is expanding shown in VMD. But the water molecules only
>>expand along x- and y- direction. The final structure is like that two
>>"plates" of water clamp the lipid cube.
>
>Did you image the trajectory before visualizing it?
>
>....dac
>
>
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Received on Wed Sep 08 2021 - 18:00:02 PDT
