[gmx-users] Error running GMX 5.14

[Sergio Manzetti]

Maybe someone can suggest a method to add ions to the system without that they appear as water molecules? 

The em looks like this: 

define = 
integrator = steep 
emtol = 100.0 
emstep = 0.0001 
nsteps = 10000 
; output frequency 
nstxout = 50 
nstvout = 0 
nstfout = 0 
nstlog = 50 
nstenergy = 50 
nstxtcout = 0 
xtc_grps = system 
; 
nstlist = 10 
pbc = xyz 
rlist = 1.4 
cutoff-scheme = group 
coulombtype = PME 
rcoulomb = 1.4 
vdwtype = cut-off 
rvdw = 1.4 
DispCorr = EnerPres 
; 
constraints = none 
constraint_algorithm = LINCS 
implicit_solvent = no 
E_x = 
E_y = 
E_z = 






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: "Smith, Micholas D." <smithmd at ornl.gov> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Tuesday, June 20, 2017 2:09:08 PM 
Subject: Re: [gmx-users] Error running GMX 5.14 

What does your *.mdp file look like? Its hard to judge what the next step should be from what you've given so far. 

-Micholas 

=================== 
Micholas Dean Smith, PhD. 
Post-doctoral Research Associate 
University of Tennessee/Oak Ridge National Laboratory 
Center for Molecular Biophysics 

________________________________________ 
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sergio Manzetti <sergio.manzetti at fjordforsk.no> 
Sent: Tuesday, June 20, 2017 7:48 AM 
To: gmx-users at gromacs.org 
Subject: [gmx-users] Error running GMX 5.14 

Hi, I have a system with DNA and water, and given the charge of the DNA of -20, genion was used to add +20 charge to the gro file. The energy minimization step gives then a warning: 

WARNING 2 [file em.mdp]: 
The sum of the two largest charge group radii (16.704304) is larger than 
rlist (1.200000) 



Which is the ignored using maxwarn option. 

When getting to the em step: 

Fatal error: 

step 25: Water molecule starting at atom 31535 can not be settled. 
Check for bad contacts and/or reduce the timestep if appropriate. 




What is the best approach here to correct this? 

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 
[ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] 

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