[gmx-users] hole in the simulation box

Dallas Warren dallas.warren at monash.edu
Tue Aug 1 00:11:02 CEST 2017

There are insufficient waters in the box to fill it up completely.

Two solutions that come to mind, add more water so it reaches the
appropriate simulated density under those conditions, or run under NPT
until reaches appropriate simulated density then swap back to NVT.
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 31 July 2017 at 18:14, edesantis <edesantis at roma2.infn.it> wrote:
> Hi gromacs users,
> I am trying to simulate a crystal supershell (5x5x5 unit cells) with martini
> ff in gromacs 5.
> I build the system in aa representation, then I converted it in CG using the
> martinize.py script,
> following the tutorial, I've done a brief equilibration in water, the after
> the solvatation of the system with non-polarizable water, I've perform
> another energy minimization followed by the equilibration.
> then I've performed md simulation in the NVT ensemble.
> It happened that during the first steps of md, an empty (no protein no
> water) hole was created in my simulation box. during the md simulation the
> hole size became bigger (this hole doesn't appear if I do the simulation in
> NPT, but I'd prefer to avoid this ensemble since a dynamic volume of the box
> could alter the reticolar parameters of my crystal),
> I've tried to calculate forces using different algorithms but the hole is
> formed every time.
> the density of my system is 1.1 times the experimental one.
> Do you have an idea of the reason why I found this hole? do you have any
> suggestion to avoid its formation??
> thank you in advance,
> regards
> Emiliano De Santis
> --
> Emiliano De Santis
> --
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