[gmx-users] segmentation fault with fitted gro files

[Marta Murcia]

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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