[gmx-users] Crystallization of NaCl saturated aqueous solution under high temperature of low pressure.
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
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
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.
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!
Visiting Ph.D Candidate
Department of Mechanical Engineering, University of Minnesota, Twin Cities.
Email: pengx288 at umn.edu
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