[gmx-users] segmentation fault with fitted gro files
David van der Spoel
spoel at xray.bmc.uu.se
Sat May 20 22:40:32 CEST 2006
Marta Murcia wrote:
> 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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>
>
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Maybe you did a modification of the protein conformation without
modifying the solvent. Try doing a minimization before the mdrun.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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