[gmx-users] too much warnings and notes

[Justin Lemkul]

On 10/29/12 10:57 AM, Albert wrote:
> On 10/29/2012 03:56 PM, Carsten Kutzner wrote:
>> Hi,
>>
>> find the reason for the warnings in your mdp file settings
>> and adjust them accordingly.
>>
>> You can also override the warnings with the -maxwarn <number>
>> option in grompp.
>>
>> Carsten
> Hello Carsten:
>
> thanks for kind reply.
>
> the only thing I confused is the last one:
>
> NOTE 4 [file md.mdp]:
>    The sum of the two largest charge group radii (0.597592) is larger than
>    rlist (1.000000) - rvdw (1.200000)
>
>

It is related to Note 3, which indicates you have a very large charge group. 
You will have artifacts related to neighbor searching (and potentially poor 
energy conservation) if you use such large groups.  There is discussion on this 
note on the Gromacs website and in the list archive.  I post the link to the 
Errors page daily, so surely you can find it :)

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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