VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Fri Jan 29 2016 - 13:36:24 CST

Thanks a lot!!

After running this command

solvate -minmax {{-50 50 -50} {50 50 50}} -o water_box

I am getting the following error:

Couldn't load output files. Please make sure that you have enough disk
space, and that you didn't set solvent box boundaries that would
produce zero placed waters.

How should I address it?

Also, is there a way to create a box filled with atoms/molecules other
than water?

On Fri, Jan 29, 2016 at 2:26 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
> package require solvate
> solvate -minmax {{-50 -50 -50} {50 50 50}} -o water_box
>
>
>
>> On Jan 29, 2016, at 13:17, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>
>> Hi all,
>>
>> I would like to create a simple rectangular simulation box filled with
>> spherical particles (such as Argon atoms) for testing purposes. What
>> would be the easiest way to create such system? Is it even possible
>> with vmd or namd?
>>
>> At this point, I can only think of using a solvate plugin and creating
>> a box around small protein, then deleting the protein and
>> equilibrating the box without it, but this doesn't seem optimal. Is
>> there another plugin/method that would be more suitable?
>>
>> Thanks in advance!
>>
>> Olga
>