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
[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]
<mailto:[email protected]>
============================================
--
========================================
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
========================================
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