[gmx-users] Error running GMX 5.14

[Smith, Micholas D.]

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

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