[gmx-users] Genion

[Sergio Manzetti]

Indeed, thanks: I did it manually. 

Will try updating the top with genion, 

Sergio 


Sergio Manzetti 

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From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Wednesday, June 21, 2017 4:53:59 PM 
Subject: Re: [gmx-users] Genion 

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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