[gmx-users] Genion

[Justin Lemkul]

On 6/21/17 10:30 AM, Sergio Manzetti wrote:
> Hello, genion worked, and grompp was used to run the output conf from genion. Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no longer contains the Na Cl ions added to the system. When setting up the simulation, the input confout.gro has no Na Cl ions, and the procedure is therefore not working.
> 
> Why is this so? Does one have to do the genion procedure each time one wants to use gromp with a new mdp file?
> 

You run genion once to add ions to your system.  Please provide the exact 
sequence of commands you're using.  It's very hard to follow what you're 
describing.  mdrun cannot delete anything, so "no longer contains the Na Cl 
ions" is impossible.  Either the ions are there in the beginning or they're not. 
  If you're using mdrun to run the .tpr file you're sending to genion, don't. 
There's no point.  That .tpr file is not for a simulation, it's just for genion.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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