[gmx-users] Genion

[Sergio Manzetti]

THanks Justin. 


Sergio Manzetti 

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From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Thursday, June 22, 2017 2:29:40 PM 
Subject: Re: [gmx-users] Genion 

On 6/22/17 8:22 AM, Sergio Manzetti wrote: 
> Thanks, Worked out. Now I got a note saying: 
> 
> NOTE 1 [file em.mdp]: 
> The group cutoff scheme is deprecated since GROMACS 5.0 and will be 
> removed in a future release when all interaction forms are supported for 
> the verlet scheme. The verlet scheme already scales better, and it is 
> compatible with GPUs and other accelerators. 
> 
> 
> 
> Fatal error: 
> 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. 
> This usually means that your system is not well equilibrated. 
> For more information and tips for troubleshooting, please check the GROMACS 
> website at http://www.gromacs.org/Documentation/Errors 
> 
> 
> 
> How can I fix the system, when the energy minimization step cannot? 
> 

You haven't provided any information about the force field you're using, .mdp 
settings, etc. so there's nothing to go on. If this is an immediate failure, 
visualize your starting coordinates because there's something wrong. Otherwise, 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System 

-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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