[gmx-users] Error running GMX 5.14

[Justin Lemkul]

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

-- 
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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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