[gmx-users] LINCS Warning with MDRUN - Segmentation Fault

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 17 10:43:46 CEST 2006

Gaurav Chopra wrote:
> Hi
> I am getting the following error with mdrun. I have done a few things 
> but the system complains of 1-4 interactions and gives LINCS warning if 
> the constraints are not turned off in the mdp file. I also changed the 
> fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I 
> get 1-4 interaction table size error and then LINCS warning. The output 
> of mdrun for one of these peptides is as follows. I am working on normal 
> mode decoys of each peptide and many of the decoys have no problems with 
> mdrun but some gives this error and Segmentation Fault.
> Please advice.
you need to minimize better, but if your structures are really bad it 
won't help either (e.g. when you have a sidechain sticking through a ring)

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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