[gmx-users] hole in the simulation box

edesantis edesantis at roma2.infn.it
Mon Jul 31 10:14:59 CEST 2017

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,
Emiliano De Santis

Emiliano De Santis

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