[gmx-users] Largest charge group radii for Van der Waals; Largest charge group radii for Coulomb

[Justin A. Lemkul]

Javier Cerezo wrote:
> Hi Tom
> 
> This warning comes from a check that (I think) was not present in 4.0.7 
> version. This problem is usually a consequence of bad charge group 
> numbering in your topology. Please, provided your topology file and 
> grompp command arguments.
> 

It is also possible that the charge group is split across PBC, causing it to be 
broken.  In this case, nothing is wrong.  Using a plain cutoff, however, 
generally is very wrong...

-Justin

> Cheers
> Javier
> 
> El 11/06/11 05:59, Tom escribió:
>> Dear Gromacs Users,
>>
>> My file has no problem when i grompp with verison of 4.0.7
>>
>> When i swith to Gromacs  4.5.3 and grompp my file, it gives this reports:
>> ----------------------------------------------------------------
>>    NOTE 3 [file grompp.mdp]:
>>    You are using a plain Coulomb cut-off, which might produce artifacts.
>>    You might want to consider using PME electrostatics.
>>
>>
>> Largest charge group radii for Van der Waals: 4.986, 4.983 nm
>> Largest charge group radii for Coulomb:       6.719, 6.712 nm
>>
>> WARNING 1 [file grompp.mdp]:
>>    The sum of the two largest charge group radii (13.430987) is larger 
>> than
>>    rlist (1.200000)
>> ----------------------------------------------------------------------------------- 
>>
>>
>> Is there anyone who can help see why different version mak such
>> problem? How to solve the problem?
>>
>> Thanks a lot!
>>
>> Tom
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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