[gmx-users] IONs + PME run problem!!
Michael Brunsteiner
mbx0009 at yahoo.com
Tue Feb 17 10:08:01 CET 2004
--- "Mungikar, Amol Arvind (UMR-Student)" <mungikar at umr.edu> wrote:
> Dear gmx-users,
> I am here again with another problem. I was trying to run a model
> peptide + ions in water. The system is electroneutral. I was trying
> to do a 2 ns md run.
> md.mdp file:
>
> cpp = /lib/cpp
>
> constraints = all-bonds
>
> integrator = md
>
> dt = 0.002 ; ps !
>
> nsteps = 1000000; total 2 ns.
>
> nstcomm = 1
>
> comm_grps = Protein SOL Na
You constrain the COM of several different groups
in one system. I could imagine that this causes the
problem. The Na ions, for example, are moved in a concerted
fashion by a small distance at each time-step independently
of the the positions of the atoms in the SOL and the Protein
groups ... rather unlikely to happen I admit, just a wild guess ...
but even if this is not the problem, I would not constrain the COMs
separately for each group anyway (at least not in a system that is
"relatively" isotropic, such as yours)
To me there seems to be no good (physical) reason for doing so,
might give you artefacts ...
FWIW
mic
> nstxout = 5000
>
> nstvout = 5000
>
> nstfout = 0
>
> nstlog = 500
>
> nstenergy = 500
>
> nstlist = 500
>
> ns_type = grid
>
> rlist = 1.0
>
> coulombtype = PME
>
> rcoulomb = 1.0
>
> rvdw = 1.0
>
> ; nose-hoover temperature coupling is on in two groups
>
> Tcoupl = nose-hoover
>
> tc-grps = Protein SOL Na
>
> tau_t = 0.1 0.1 0.1
>
> ref_t = 300 300 300
>
> ; Energy monitoring
>
> energygrps = Protein SOL Na
>
> ; Isotropic pressure coupling is now on
>
> Pcoupl = no
>
> Pcoupltype = isotropic
>
> tau_p = 0.5
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> ; Generate velocites is off at 300 K.
>
> gen_vel = yes
>
> gen_temp = 300.0
>
> gen_seed = 173529
>
> EM output
>
> Steepest Descents converged to 100 in 724 steps
>
> Potential Energy = -3.69708e+04
>
> Maximum force: 9.12667e+01
>
>
> MD run output:
> t = 383.000 ps: Water molecule starting at atom 1300 can not be
> settled.
>
> Check for bad contacts and/or reduce the timestep.Wrote pdb files
> with previous and current coordinates
>
> Energies (kJ/mol)
>
> Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
>
> 1.10620e+02 5.17073e+01 5.82271e+01 3.68468e+01 1.18949e+03
>
> LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En.
>
> 2.35068e+06 -3.19766e+04 -5.70743e+03 2.31444e+06 nan
>
> Total Energy Temperature Pressure (bar)
>
> nan nan nan
>
> Fatal error: ci = -2147483648 should be in 0 .. 124 [FILE nsgrid.c,
> LINE 210]
>
> It says me to reduce the timestep, I didnt understand this, why?
>
> Am I doing anything wrong with "md.mdp" file!! or the energy
> minimization is creating a problem.
>
> Thank you very much for your help!
>
> Amol A Mungikar
>
>
>
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