[gmx-users] grompp bug (system charge)

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Mon Apr 28 10:10:01 CEST 2003

Hello David,

David wrote:
> On Sun, 2003-04-27 at 12:26, Christoph Freudenberger wrote:
>>hi there,
>>There seems to be a bug in the way grompp calculates the total
>>charge of the system.
>>For my box (9 kations/9 anions/some 10000 solvents) grompp prints
>>out a warning:
>>WARNING 4 [file "topol.top", line 22]:
>>   System has non-zero total charge: 7.999992e+00
>>I dublechecked the charges in the resulting tpr using the following
>> > gmxdump -s test.tpr |grep "atom\["|awk -F, '{print $5}'|awk -F= '{sum+=$2}END{print sum}'
>>and get:
>>which is neutral to me.
> can you include the topology?

Sure... I suppose you need topol.top and all the inclueded itp's.
Should I send them to you in a mail or post them to the list?

I have noticed some problems with the total charge in grompp already
some time ago but the 'erroneous' charge was in the range of ~1e+05 then.
I ignored it because I thought it was a roundoff error.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

More information about the gromacs.org_gmx-users mailing list