[gmx-users] mdrun errors out

[David]

On Tue, 2002-08-13 at 20:22, Peter C. Lai wrote:
> hi folks,
> I pretty much used the "Getting started" section as a template
> for setting up the mdrun. I solvated my protein, minimized,
> and tried to mdrun. The first indication of trouble is lots of:
> 
> Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         NaN,          NaN,          NaN}
>             Box[    1]={         NaN,          NaN,          NaN}
>             Box[    2]={         NaN,          NaN,          NaN}
>          Can not fix pbc.
> 
> It then quits with:
> Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]

Most likely your input structure. Check it using rasmol or so. Also look
at the energy in minimization. Is it negative? (-41 * number of water
molecules)

> 
> If I change the ns_type to SIMPLE, it claims that twinneighbor
> searching using simple algorithm is not implemented.
> 
> other notes: i used genconf to build the rectangular box. hasn't
> given me any issues during minimization, only when trying to mdrun.
> 
> http://cowbert.2y.net/~sirmoo/yale/md/dev/200208131320/pr.mdp
> if anyone is interested.
> 
> thanks,
> pete
> 
> -- 
> Peter C. Lai
> University of Connecticut
> Dept. of Molecular and Cell Biology | Undergraduate Research Assistant
> Yale University School of Medicine
> Center for Medical Informatics | Research Assistant
> http://cowbert.2y.net/
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++