[gmx-users] Error running GMX 5.14

[Sergio Manzetti]

Precisely. Thanks. 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
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From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Tuesday, June 20, 2017 4:42:37 PM 
Subject: Re: [gmx-users] Error running GMX 5.14 

On 6/20/17 10:36 AM, Sergio Manzetti wrote: 
> One simple question, where does one get the sytem input for genion, as it only want tpr, unless one uses grompp? 
> 

Yes, you have to use grompp on the solvated system to get a .tpr of the system 
that contains no ions. You pass that .tpr to genion and then never use it again. 

-Justin 

> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] 
> 
> 
> 
> From: "Justin Lemkul" <jalemkul at vt.edu> 
> To: "gmx-users" <gmx-users at gromacs.org> 
> Sent: Tuesday, June 20, 2017 4:39:03 PM 
> Subject: Re: [gmx-users] Error running GMX 5.14 
> 
> On 6/20/17 10:32 AM, Sergio Manzetti wrote: 
>> Let me see if I have it right. 
>> 
>> After doing the minimization of the system without ions, I add ions to the minimized system and replace the waters. 
>> 
> 
> I see no point in doing multiple rounds of minimization like this. Just build 
> the whole system and minimize. 
> 
>> Then I use grompp to set up the sim with the output tpr from the genion command as -c file, and the original topology ? 
>> 
> 
> No. The .tpr file provided to genion is never used again. It has one purpose 
> only and it is not an output from genion at all. 
> 
> This is all very basic stuff. Please try some tutorials: 
> 
> http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use 
> 
> -Justin 
> 
>> Sergio 
>> 
>> 
>> Sergio Manzetti 
>> 
>> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
>> 
>> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
>> Midtun 
>> 6894 Vangsnes 
>> Norge 
>> Org.nr. 911 659 654 
>> Tlf: +47 57695621 
>> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] 
>> 
>> 
>> 
>> 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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