[gmx-users] IONs + PME run problem!!

[Michael Brunsteiner]

--- "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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