[gmx-users] TIP4P and ions
David van der Spoel
spoel at xray.bmc.uu.se
Fri Sep 3 10:00:52 CEST 2004
On Fri, 2004-09-03 at 06:47, Ilya Chorny wrote:
> 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
> 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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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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