[gmx-users] vdW parameters and atoms moving too fast

Nicolas SAPAY nsapay at ucalgary.ca
Tue Feb 6 23:35:42 CET 2007

Hello everybody,

I'm still fighting with the CHARMM implementation in GROMACS. I have
discover  discrepancies in some LJ/LJ1-4 energies and have perform some
basic test to see if the problem comes from my parameters or the way I use
Gromacs. So, I have built a system made of 1 OT and 1 HT non-bonded atoms
seperated by 0.1 nm to test vdW parameters (the system is not directly
relevent, it's just to make a test). Then, I have run 1 step of MD.
Initial energy values are OK : I found exactly what I should find. But
problems arise at step 1 where the atoms move too fast while kinetic
energy remains null. I have check my mdp files and everything looks OK (I
have used a small timestep of 0.0001 ps, a NVE ensemble, a Gromacs
compiled with double precison, ...). Finally I don't understand why atoms
move so fast with no kinetic energy. So, I wonder if my system is not "too
simple" and leads to initialiation problems, or if there is some problem
of accuracy with non bonded energy when atoms becomes too close and should
relax, or I have made a too evident mistake that I cannot fix...



[ Nicolas Sapay Ph.D. ]
University of Calgary, Dept. of Biological Sciences
2500 University Dr. NW, Calgary AB, T2N 1N4, Canada
Tel: (403) 220-6869
Fax: (403) 289-9311

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