[gmx-users] TIP4P and ions

[David van der Spoel]

On Fri, 2004-09-03 at 06:47, Ilya Chorny wrote:
> Hello
> 
> 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 :)
maybe LJ repulsion is too low. Compare parameters to those for Na+ and
Cl-
> 
> Cheers
> 
> Ilya
> 
> 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
> 1.05091
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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