VMD-L Mailing List

From: Ryan Woltz (rlwoltz_at_ucdavis.edu)
Date: Fri Oct 22 2021 - 23:34:08 CDT

Hi Ashar,

       I hope this is correct. I found this in file input.config.dat

{"systype":"bilayer","dimensions":["145.078088","145.078088","144.858064","90.0","90.0","90.0"],"input":["namd"],"forcefield":{"type":"c36m","files":["default"],"custom":[]},"hmr":false}

So I believe my boundaries are "145.078088","145.078088","144.858064" and
compared to your calculations of 180 188 158 these do not match up, correct?

For clarification, the charmm-gui of 135-145 is the approximate x,y,z
dimensions you give Charmm-gui to create a system for you. So each system I
have (9 of them) I used the input range from 135-145 angs depending on the
system. For this system I'm using as an example I think I used 145 but
there are others that are around 135. Sorry for the confusion, I think this
is irrelevant information and whatever we fix in this system I can apply to
the others.

Did I understand what you are asking for with periodic boundaries? I looked
at the link but I'm pretty new to the scripting part of MD. I tried to
implement wrapAll and pbc wrapAll into the console with no luck. Apologies
for being new to this.

Thanks,

Ryan

On Fri, Oct 22, 2021 at 8:15 PM Ashar Malik <asharjm_at_gmail.com> wrote:

>
> 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
>
>>