[gmx-users] atomnumber=-12345

[Itamar Kass]

Hi Dallas,

Thank for the replay. I think that I found what was "wronge". I have 
created the tpr files using GROMACS 3.3.3 but used gmxdump (-sys) from 
the GROMACS 4.0.5 package, not a very smart thing to do, ha?  I guess 
this was the source of my error.


Thanks,
Itamar


On 21/01/10 1:36 PM, Dallas B. Warren wrote:
>
> 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
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to 
> resemble a nail.
>
> *From:* gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] *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: Itamar.Kass at med.monash.edu.au 
> <mailto:Itamar.Kass at med.monash.edu.au>
> ============================================
>

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