[gmx-users] atomnumber=-12345

[Justin A. Lemkul]

Itamar Kass wrote:
> 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.

The .tpr file format changed between the 3.3.x and 4.0.x version series, so that 
is probably the reason, yes.

-Justin

> 
> 
> 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>
>> ============================================
>>
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================