[gmx-users] hole in the simulation box

edesantis edesantis at roma2.infn.it
Wed Aug 2 14:11:30 CEST 2017

thank you for your suggestion,

I've tuned the gmx solvate -radius parameter until I achieved the 
stability of the box dimensions in the NPT ensemble, now it seem the 
everything is working...

thanks again,


On 2017-08-01 00:10, Dallas Warren wrote:
> 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
>> --
>> Gromacs Users mailing list
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Emiliano De Santis

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