[AMBER] problem deriving implicit polarised charges charges with mdgx

From: Luis Simon <lsimon.usal.es>
Date: Fri, 5 Feb 2021 22:10:59 +0100

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.



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Received on Fri Feb 05 2021 - 13:30:02 PST
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