Hi Surma,
> I am trying to equilibriate a system of one CN- ion and one Na+ atom in
> TIP4P water box. I added the charges in CN- by Gaussian (g09) and used
> ff03
> forcefield. The box sizes are 15.408, 15.517, 19.057. The system has
> 107
> water molecules. I need these specific parameters (as I am trying to
> reproduce an already published work). I am getting an error while
> equilibrating at constant volume:
>
>
> Ewald PARAMETER RANGE CHECKING:
> parameter skinnb+cutoffnb: (nonbond list cut) has value 0.80000E+01
> This is outside the legal range
> Lower limit: 0.00000E+00 Upper limit: 0.77042E+01
> Check ew_legal.h
Your box size is too small. Especially if this is your initial size which
will then shrink when you run constant volume.
> I have tried changing the cut=7.5, cut=7.0, cut=6.0 --> every value
> gave me
> same error. Lowering the ewald cut further gives segmentation fault. I
Do NOT EVER reduce cut below 8.0. This is an absolute no no and will lead to
significant errors in the results due to truncation of the VDW interactions.
Parts of the code are likely not tested below 8.0 angstroms cutoff either
although I suspect your segfault comes from your system blowing up or some
similar problem happening because of the truncation of the interactions.
> do
> not want to change the box size and number density (as I realise they
> are
> quite small), so I need help in dealing with this error.
There is nothing you can do except increase the size of your box. I suggest
adding more water molecules to give you a box of at least 20 x 20 x 20 or
so, that should be safe, maybe 150 water molecules or so. Sorry but there is
nothing else you can do without seriously compromising the accuracy of your
calculation. If the published work used such a small box then I would be
VERY suspicious of it. Take a careful look at what their protocol actually
was. Did they use PME for example?
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Mon May 02 2011 - 02:00:03 PDT
