[gmx-users] Crystallization of NaCl saturated aqueous solution under high temperature of low pressure.

[Justin Lemkul]

On 9/10/17 6:28 PM, Yanke Peng wrote:
> Hello to all,
> 
> 
> 
> I am a beginner of MD simulation and trying to do some inorganic salt
> crystallization simulation.
> 
> 
> 
> I am trying to simulate the crystallization process of NaCl saturated
> aqueous solution by the evaporation of solvent - water molecules under high
> temperature or low pressure.
> 
> 
> 
> Basic settings: 352 water molecules in a 2.5*2.5*2.5 nm box;  For a
> saturated solution, 32 Na+ and 32 Cl- should be introduced by replacing 64
> water molecules.
> 
> 
> 
> Below are the problems I encountered.
> 
> 
> 
> 1.     gmx genion only could replace 37 water molecules with 32 Na+ and 5
> Cl-.  Does this means gmx genion couldn’t generate saturated solution
> sometimes? So, I used Avogadro to generate a coordinate file of saturated
> NaCl solution and then generated a .gro file by the coordinate file.
> 

genion will do what its told - what command did you issue that gave such a 
result?  A simple use of -np 32 -nn 32 should add 32 cations and anions to the 
system.  There are clearly enough waters to replace with ions, so there should 
be no issue.

> 2.     During the energy minimization,  I chose integrator=steep in em.mdp
> and after 13 steps, the process stopped.  Here is the error information.
> 
> Fatal error:
> 
> step 14: Water molecule starting at atom 22 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> 
> 3. I changed the integrator=md and no error information showed up during
> the -mdrun.  However, the em.trr file is empty.  So when I rum the grompp
> during the equilibration NVT, the error information said "Number of atoms
> in Topology is not the same as in Trajectory".
> 

Trying to run dynamics on a system that refuses to energy-minimize is a futile 
venture.  If the system is not stable enough to minimize, dynamics will 
similarly fail because you're at some high-energy, unphysical point.

What grompp command did you enter to get such an error?  Please always report 
exact commands when seeking help.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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