VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Oct 22 2021 - 22:15:11 CDT

Hi,

> $ minmax 0
> {-104.74568176269531 -113.04422760009766 -86.82054138183594}
> {76.17849731445313 75.81551361083984 72.08464813232422}
>
>
>From here your system size (approximately) along x, y and z are

76 - (-104) = 180
75 - (-113) = 188
72 - (-86) = 158

set a 141.104004
> set b 141.104004
> set c 144.858064
>
>
This is you just assigning three values to three variables.
Where are these values used?
The values that I calculated roughly should be your basis vectors for
periodic boundaries.

See this:
https://www.ks.uiuc.edu/Research/namd/2.9/ug/node33.html

Are they in your config file?

> In charmm-gui when setting up the system I did enter 135-145 for the
> initial size estimate for each side depending on the system so I think it
> matches up.
>

I am not familiar with the charmm-gui so not sure what 135-145 means.

> Was this what you were looking for? Any other information I can provide
> you with that would help in your assistance?
>

Find the section in your config file where you set up your boundary
conditions.

Regards,
Ashar

>