[gmx-users] TIP4P and ions

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Fri Sep 3 06:47:10 CEST 2004


I am having difficulty equilibrating a simulation of TIP4P water and two
oppositely charged ions.
The ions have Lennard Jones Parameters corresponding to united atom methane
but with a charge of +1 and -1.
When I turn off the charges the system behaves just fine and it also behaves
just fine if I use SPC. I am running an
NPT simulation with PME. I am using Lincs to constrain the bonds. I have
about 2000 TIP4P water molecules and 2 ions.
Any help is greatly appreciated :)



My output from the simulation is as follows:

Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting mdrun 'Generated by Ilya Chorny to view H2O-Solute angles in water'
5000 steps,     10.0 ps.

Back Off! I just backed up traj.trr to ./#traj.trr.2#

Step 127, time 0.254 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 26.108976 (between atoms 4940 and 4939) rms 0.472240
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4939   4938  111.5    0.1521   0.4181      0.1514
   4940   4938   90.5    0.0964   2.5721      0.0957
   4940   4939   90.5    0.0968   2.5949      0.0957
Wrote pdb files with previous and current coordinates

Step 128  Warning: pressure scaling more than 1%, mu: 1.05091 1.05091

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