Re: [AMBER] problem deriving implicit polarised charges charges with mdgx

From: Luis Simon <>
Date: Sun, 7 Feb 2021 22:29:15 +0100

I have found a solution, so I will reply myself just in case someone reaches the original message with a similar problem.

The problem was that the crd file that I was using for input did not contain cell information. It was solved by adding “ntxo=1” to the &control directive in the input file that I used to generate that file.

Regarding the number of processors, it is set automatically if the MPI version of mdgx is used, with the number of processors specified to launch the mdgx. However, it is limited to 8 processors.

> On 5 Feb 2021, at 22:10, Luis Simon <> wrote:
> I am following the tutorial to get the IPQ charges with mdgx, but while trying to prepare the grid of solvating waters I obtain the following message:
> CreateCellGrid >> Error. Cell grid must be at least two cells in all
> CreateCellGrid >> dimensions such that the simulation cell is at least
> CreateCellGrid >> twice the nonbonded cutoff in all dimensions. This likely
> CreateCellGrid >> occurred because the simulation system is too small.
> My system is bigger than the glicerol molecule in the tutorial, so the first thing that I tried was to increase (up to a factor of 50) the unx, uny and unz values in the mdgx input file, but the error message repeats. I prepared the crd file for input to mdgx using a cubic box 12A apart from any solute atom, and the cutoff that I used in the equilibration was 9A.
> I also wonder if there is a way of obtaining orca input files instead of letting the program to run the orca calculation. That may help to schedule things in a queue and to have more control on the input settings (I am thinking on the RI options in orca). I have read in the manual that keepQMInput will not delete the input file generated, and somehow I guess that it could be possible to kill the QM calculation, but I do not know how the automated translation to cube file format will be done.
> A final question is how to control the number of proccessors in which the calculation will run.
> Thanks
> Luis

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Received on Sun Feb 07 2021 - 13:30:01 PST
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