[gmx-users] Error running mdrun em with Sodium ions in GMX 5.14

2017-06-20 Thread Sergio Manzetti 


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 (1.20) 



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. 


However, these are not waters, but there are sodium ions added to the system by 
replacing 20 water molecules, which grompp thinks are waters. The index file 
does not contain info about these, as also there, the Sodium are not identified 
and differentiated from water molecules. 


What is the best approach here to correct this? 

Thanks! 

Sergio Manzetti 

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Re: [gmx-users] Error running mdrun em with Sodium ions in GMX 5.14

2017-06-20 Thread Justin Lemkul 



On 6/20/17 8:04 AM, Sergio Manzetti wrote:



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 (1.20)



This probably means the initial coordinates are broken across PBC.




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.


However, these are not waters, but there are sodium ions added to the system by 
replacing 20 water molecules, which grompp thinks are waters. The index file 
does not contain info about these, as also there, the Sodium are not identified 
and differentiated from water molecules.



grompp will only think sodium ions are waters if your topology is broken and 
you've overridden some kind of error.  Make sure your coordinates and topology 
are consistent.  grompp and mdrun only do what they're told; they can't possibly 
invent some conversion between waters and sodium.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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