[gmx-users] segmentation fault with fitted gro files
Marta Murcia
mam2070 at med.cornell.edu
Sat May 20 22:11:46 CEST 2006
This is the md.log, note that the problem is with SOL (namely water)
t = 0.000 ps: Water molecule starting at atom 171088 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Large VCM(group Protein): 0.00000, 0.00000, 0.00000,
ekin-cm: 1.26591e-12
Large VCM(group SOL): nan, nan, nan,
ekin-cm: nan
Large VCM(group NA+): -0.04876, -0.04099, 0.09954,
ekin-cm: 2.08686e+00
Large VCM(group CA): 0.04345, -0.03030, -0.15215, ekin-cm:
3.12094e+00
Large VCM(group MG): -0.19705, -0.24462, -0.29635, ekin-cm:
2.26636e+00
Large VCM(group rest): -0.01463, -0.02202, -0.04427,
ekin-cm: 1.10597e+00
Long Range LJ corr.: <C6> 3.3051e-04
Long Range LJ corr.: Epot -6744.31, Pres: -128.705, Vir: 6744.31
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
2.93325e+04 1.68546e+03 1.19906e+04 2.20380e+04 8.49336e+04
LJ (SR) LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.
2.07755e+16 -9.80171e+03 -6.74431e+03 -2.26739e+06 -4.58131e+05
Potential Kinetic En. Total Energy Temperature Pressure (bar)
2.07755e+16 nan nan nan nan
Marta Murcia wrote:
>
>
> David van der Spoel wrote:
>
>> Marta Murcia wrote:
>>
>>> Hi again,
>>> sorry about that, what I meant is that before even doing grompp I am
>>> taking snaphots that I oriented with respect a particular
>>> conformation (with trajconv or vmd) so I use gro files for the afm
>>> pulling that correspond to fitted structures instead of the raw
>>> files that would come out just by cutting the trajectory (with these
>>> there is no seg. fault at all)
>>
>>
>>
>>
>> ok, then you should be more specific on the error. What happens,
>> when? Try running with -debug and check the mdrun.log file
>
>
>
>
>
>
> David thanks again,
>
> I am getting the following message just after the starting of the
> dynamics (pull.pdo is not even written although the input is read
> fine, traj.xtc is started and written until it crashes)
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.000302 (between atoms 5076 and 5096) rms nan
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
>
> Back Off! I just backed up step-1.pdb to ./#step-1.pdb.1#
>
> Back Off! I just backed up step0.pdb to ./#step0.pdb.1#
> Wrote pdb files with previous and current coordinates
> Segmentation fault
>
> this is what says the log file
> ======================
> TC: group 0: T: 302.527, Lambda: 0.999916
> TC: group 1: T: 300.265, Lambda: 0.999991
> constraint virial (3x3):
> constraint virial[ 0]={ nan, nan, nan}
> constraint virial[ 1]={ nan, nan, nan}
> constraint virial[ 2]={ nan, nan, nan}
> dekin (3x3):
> dekin[ 0]={ nan, nan, nan}
> dekin[ 1]={ nan, nan, nan}
> dekin[ 2]={ nan, nan, nan}
> ekin (3x3):
> ekin[ 0]={ 1.42945e+05, -3.70738e+02, 9.92575e+00}
> ekin[ 1]={-3.70738e+02, 1.42321e+05, 1.46772e+02}
> ekin[ 2]={ 9.92558e+00, 1.46772e+02, 1.42120e+05}
> dekin = nan, ekin = 427386 vcm = ( nan nan nan)
> mv = ( nan nan nan)
> PC: pres (3x3):
> PC: pres[ 0]={ nan, nan, nan}
> PC: pres[ 1]={ nan, nan, nan}
> PC: pres[ 2]={ nan, nan, nan}
> PC: ekin (3x3):
> PC: ekin[ 0]={ nan, nan, nan}
> PC: ekin[ 1]={ nan, nan, nan}
> PC: ekin[ 2]={ nan, nan, nan}
> PC: vir (3x3):
> PC: vir [ 0]={ nan, nan, nan}
> PC: vir [ 1]={ nan, nan, nan}
> PC: vir [ 2]={ nan, nan, nan}
> PC: box (3x3):
> PC: box [ 0]={ 1.04192e+01, 0.00000e+00, 0.00000e+00}
> PC: box [ 1]={ 0.00000e+00, 1.04192e+01, 0.00000e+00}
> PC: box [ 2]={ 0.00000e+00, 0.00000e+00, 1.60387e+01}
>
> I guess I have a problem whit the box
>
>
>
>
>>
>>> Thanks
>>> M
>>>
>>> David van der Spoel wrote:
>>>
>>>> Marta Murcia wrote:
>>>>
>>>>> Dear all,
>>>>> I am running a series of AFM simulations starting from different
>>>>> conformations taken from a trajectory (gmx 3.3). Everything works
>>>>> fine, but if I try to orient all the snapshots with respect to a
>>>>> reference (based on the protein superimposition) I get
>>>>> segmentation fault for all of them while doing mdrun, except for
>>>>> the one that I used as template in the alignment. My feeling is
>>>>> that the box of water molecules is not being well understand. I
>>>>> was using the same topology files as before but this shouldn't
>>>>> affect (should be?). Do I need to do pdb2gmx again for the
>>>>> individual gro files. Does it have something to do with genbox?
>>>>> What is wrong?
>>>>> Guys I really appreciate your help, I don't know what to do but
>>>>> I'd bet there is something really stupid I am missing
>>>>
>>>>
>>>>
>>>>
>>>> it's not clear what you are doing. how can you "orient snapshots
>>>> in mdrun"?
>>>>
>>>>> Thanks so much
>>>>> M
>>>>>
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>>>>
>>>>
>>>>
>>>>
>>>>
>>>
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>>
>>
>>
>
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