Hi Ross,
Thank you so much for your input. I do not know what you mean by PME. I
will increase the box size and try it again.
~Surma
On Mon, 2 May 2011 01:41:57 -0700, "Ross Walker" <ross.rosswalker.co.uk>
wrote:
> 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 - 09:00:05 PDT
