Might be a good idea to provide the input and output that generated the error.
Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of Itamar Kass Sent: Thursday, 21 January 2010 11:13 AM To: Discussion list for GROMACS users Subject: [gmx-users] atomnumber=-12345 Hi, After one of my simulation had crashed, I had used gmxdump to look into it. What stoke me was the all atoms have the same atomnumer: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q= 1.29000e-01, mB= 1.40067e+01, qB= 1.29000e-01, resnr= 0, atomnumber=-12345} atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01, resnr= 0, atomnumber=-12345} atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01, resnr= 0, atomnumber=-12345} atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01, resnr= 0, atomnumber=-12345} atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.30190e+01, q= 1.27000e-01, mB= 1.30190e+01, qB= 1.27000e-01, resnr= 0, atomnumber=-12345} and so on... I wonder if someone knows what the origin of this error and how to over come it? In addition, it is vary strange that the simulation run for 100ps before it crashed. All the best, Itamar. -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: [email protected] ============================================
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