On 21/08/2011 4:42 PM, meisam valizadeh kiamahalleh wrote:
Dear Justin
Thank you very much for your reply
>>Regarding Warning 1; Yes, I have introduced the new parameter for C
C bond and it is what I want.
>>Regarding Note 1; Actually, the charges for each atom in topology
file are what I incl
This is a tough issue and there are some unresolved questions here.
I recommend seeing the work of Kastenholz and Hunenberger on ion solvation
in JCP a couple years ago (two companion papers) as these explain the key
issues.
Thanks.
On Wed, Aug 17, 2011 at 3:24 AM, Marcelino Arciniega Castro <
m
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; disturbing
> > magnitude (i.e., it does not arise simply due to floating point
> > arithmetic),
> > indicating that the charges assigned in the topology are junk.
> >
> > > 3) Regarding Note 2, Is there anything wrong with my mdp file or
> >
t; processor is too small for this calculation, I may be able to
> work with
> > our cluster if it is advised.
>
> For minimization, this often happens. It is unimportant in
this case.
>
> -Justin
>
> >
> > Thank you very much
> > Best regards
> > M.V.K
> >
>
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