[gmx-users] Charge Group Number in itp File (cgnr)
Mark.Abraham at anu.edu.au
Tue Sep 11 02:53:32 CEST 2012
On 11/09/2012 7:55 AM, Andrew DeYoung wrote:
> In the [ atoms ] section of an .itp file, there is a column (cgnr) where a
> charge group number is given (an integer). This cgnr column is shown in,
> for example, the manual version 4.5.4 in Section 5.7.
> My question is, do the charge group numbers have to be _consecutive_
No, where relevant they need only differ from the previous group. A
casual look at the code suggests that consecutive atoms listed with
charge groups 1 2 1 2 1 2 respectively will end up 6 different charge
> For some reason, I just noticed after running many simulations that the .itp
> file for one of my molecules has a missing charge group number. For
> example, the cgnr column includes the series 425, 426, 428, ... . That is,
> for some very odd reason (I must have made a typo), there is no charge group
> with number 427. Will this cause inaccuracies in the simulation? I do not
> want to rerun all the simulations unless it seems like the missing integer
> will cause problems.
I think it is highly unlikely. You can inspect the .tpr with gmxdump,
search for "cg" and have a look at the charge group distribution. You
can also construct the .itp "correctly" and re-process with grompp and
demonstrate with gmxcheck that both .tpr files are identical.
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