[gmx-users] Genion

[Sergio Manzetti]

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. 



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 4:44:16 PM 
Subject: Re: [gmx-users] Genion 

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 

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

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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