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

Yanke Peng pengx288 at umn.edu
Mon Sep 11 00:28:11 CEST 2017

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.

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".

I am trying to understand the mechanism of gromacs by learning the manual

Could you give me a clue to solve these problems? I really appreciate any
help from you!

Yanke Peng

Visiting Ph.D Candidate

Department of Mechanical Engineering, University of Minnesota, Twin Cities.

Email: pengx288 at umn.edu

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