[gmx-users] DNA simulation- Cannot fix pbc.

[Dallas Warren]

>I could solvate the protein and add 30 NA+ ions. But the MD run got
>crashed giving some errors which I am not able to debug. I am attaching
>the ("full.mdp") parameter file and the message ("log") generated by
>mdrun. I'll be thankful if anyone of you can suggest me what to do.

http://www.gromacs.org/search/index.php?query=LINCS+warning&max=20&result=normal&sort=score&idxname=gromacs_site&idxname=mailing_lists

That URL pulls up some threads on this list that deal with that sort of 
error that you are seeing.

I believe it can be either that the starting confirmation is not in a 
stable enough state or pressure coupling is too tight.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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