[gmx-users] Solvating a non-orthogonal box

[Dallas Warren]

There is no such thing as "out of the box".  You are looking at an
arbitary visual representation of the system.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

https://twitter.com/dr_dbw/status/909559339366572032

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 16 May 2018 at 02:57, Anuradha Bhat <anur.bhat at gmail.com> wrote:
> 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!
> Annu.
>
> 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.
>> *>* --
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