[gmx-users] Genion

[Justin Lemkul]

On 6/21/17 10:45 AM, Sergio Manzetti wrote:
> Hi Justin, the sequence was:
> 
> gmx editconf ....
> 
> gmx solvate ....
> 
> gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr
> 
> gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA -nname CL
> 
> then:
> 
> gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p topol_solvated -o dna_solv_NaCl_EM
> 
> gmx mdrun
> 
> 
> This worked.
> 
> Then for the sim:
> 
> dna_solv_NaCl_EM.gro does not contain any ions.
> 

You didn't pass topol_solvated.top to genion -p, so it did not update the number 
of ions.  Your final call to grompp should have triggered an error because the 
contents of the system will not match, unless you did this manually.  But again, 
it is *impossible* for mdrun to delete anything.  So check the contents of your 
files carefully, even just in a text editor for coordinates and topology, to 
make sure you have what you think you have.

-Justin

-- 
==================================================

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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