[gmx-developers] charge group size in grompp

[Jochen Hub]

On 3/30/11 Mar 30,12:46 AM, Berk Hess wrote:
> Hi,
>
> I didn't think about broken charge groups when writing the check.
> You have to do some effort to produce a configuration with broken 
> charge groups.
> But if grompp allows reading of such configurations, the checks should 
> handle
> this correctly. You can file an issue with low priority.
OK, I submitted the issue with a test system.

Thanks,
Jochen


>
> Berk
>
> On 03/30/2011 03:47 AM, Jochen Hub wrote:
>> Hi,
>>
>> when running grompp for an equilibrated lipid system in a skewed box 
>> (for having a hexagonal prism), grompp seems to compute the size of 
>> of the charge groups incorrectly, if the lipids are in a broken 
>> representation:
>>
>> Largest charge group radii for Van der Waals: 9.377, 9.375 nm
>> Largest charge group radii for Coulomb:       9.377, 9.375 nm
>> WARNING 1 [file em.mdp]:
>>   The sum of the two largest charge group radii (18.751873) is larger 
>> than
>>   rlist (1.000000)
>>
>> When I make the molecules whole by getting first a tpr and then using 
>> trjconv -pbc mol:
>>
>> grompp -p topol_pop.top -c pop.pdb -f em.mdp -maxwarn 1
>> trjconv -s topol.tpr -f pop.pdb -o popw.pdb -pbc mol
>>
>> grompp is doing ok.
>> Largest charge group radii for Van der Waals: 0.246, 0.245 nm
>> Largest charge group radii for Coulomb:       0.246, 0.245 nm
>>
>> The wrong charge group size is given in all possible until cell 
>> representations (tric, rect, and compact). When starting
>>
>> Is that a known issue? I use version 4.5.4-dev-20110321-f8688a9.
>>
>> Should I submit a bug report?
>>
>> Thanks,
>>
>> Jochen
>>
>


-- 
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Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell&  Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755
http://xray.bmc.uu.se/~jochen/index.html
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