[gmx-users] Error running GMX 5.14

[Sergio Manzetti]

Thanks Justin. So it is right to run the simulation without ions, then add ions, then re-run with ions with the new topolgy? 

Sergio 


Sergio Manzetti 

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From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Tuesday, June 20, 2017 4:21:18 PM 
Subject: Re: [gmx-users] Error running GMX 5.14 

On 6/20/17 10:14 AM, Sergio Manzetti wrote: 
> I run the simulations on the solvated DNA without adding ions. Then at the end, I added ions to the output tpr of the simulation. At this stage I waanted then to run the simulaiton with the new tpr. But that does not work. 
> 

How did you add ions to a .tpr? This implies adding them to a coordinate file, 
then adding them to the topology, and correctly compiling a .tpr with grompp. 
Depending on how you did this, it's likely the cause of your problem. 

> Is there a tutorial online on how to add Na to DNA with command line? 
> 

It's no different than any invocation of genion, which you can get from any 
tutorial. For instance: 

gmx genion -s dna_solv.tpr -o dna_solv_ions.gro -p topol.top -pname NA -np 20 

-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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