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

Nicolas SAPAY nsapay at ucalgary.ca
Wed Feb 7 01:57:14 CET 2007

good remark... here is the files! I precise that modifying the
inter-atomic distance doesn't solve the problem and that nb parameters are
defined in the ffcharm27nb.itp file as follow :

[ atomtypes ]
OT        15.9994   0.000      A  2.489540e-03  2.434767e-06
HT         1.0080   0.000      A  3.153970e-09  1.292128e-17

[ nonbond_params ]
OT     HT      1     4.382447e-05  1.371950e-09

[ pairtypes ]
OT     HT      1     4.382447e-05  1.371950e-09

I have switch off the atom charges after tested tey are not significantly
involved in my problem


<quote who="Mark Abraham">
> Nicolas SAPAY wrote:
>> 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
> I doubt it, but you can test for this readily enough... separate your
> atoms!
>> and should
>> relax, or I have made a too evident mistake that I cannot fix...
> Attaching your .mdp and .top would probably be useful here.
> Mark
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[ 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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