[gmx-users] Solvating a non-orthogonal box

Anuradha Bhat anur.bhat at gmail.com
Tue May 15 18:57:34 CEST 2018

Hi Dr. Warren,

You're right - the water does fill up the entire space when neighboring
images are turned on.

By reading online, I learned that it is okay if molecules seem to move away
from the box during the simulation and the visualization can be fixed
through the use of 'trjconv', but is it okay if the very first frame (the
initial coordinates gro file) has whole molecules outside the box?

Thank you!

This isn't a PBC issue with visualising the box, is it?  Turn on the
> neighbouring images when visualising, and you will be able to see
> quickly if the entire space is actually filled or not.
> Catch ya,
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052dallas.warren at monash.edu <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
> On 15 May 2018 at 05:21, Anuradha Bhat <anur.bhat at gmail.com <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>> wrote:
> >* Hi
> *>>* I have a box whose vectors are given by:
> *>*   (7.97262    0.00000   0.00000),  (-0.96054   2.33646  0.00000),
> *>* (15.00000          0.00000   0.00000). I would like to fill this box with
> *>* water. When I use gmx solvate to fill this box, it seems to be introducing
> *>* a rectangular shaped box of water, rather than a box of the desired shape.
> *>* Therefore, water does not fill the entirety of the box. Is there a way to
> *>* fill a non-orthogonal shaped box with the solvate command?
> *>>* Thanks in advance,
> *>* Annu.
> *>* --
> *>* Gromacs Users mailing list
> *>>* * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting!
> *>>* * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists>
> *>>* * For (un)subscribe requests visit
> *>* https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or send a mail to gmx-users-request at gromacs.org. <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>*

More information about the gromacs.org_gmx-users mailing list