[gmx-users] Crystallization of NaCl saturated aqueous solution under high temperature of low pressure.
jalemkul at vt.edu
Mon Sep 11 00:38:10 CEST 2017
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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