Hi Surma,
PME means periodic boundary calulations. For description have a look at
amber tutorial : http://ambermd.org/tutorials/basic/tutorial1/section5.htm
-Regards,
Ankita
On Mon, May 2, 2011 at 9:17 PM, <tsurma.umich.edu> wrote:
>
> 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 |
> > ---------------------------------------------------------
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> not
> > be read every day, and should not be used for urgent or sensitive issues.
>
> >
> >
> >
> >
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Received on Mon May 02 2011 - 22:30:02 PDT
