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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