Dear all, I'm resending this message (please see below) with some additional info, hoping that someone can at least point me to what I should check.
I ran the simulation with the -debug flag and got some "nan" values in mdrun.log: dekin = nan, ekin = 175815 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]={ 5.66646e+04, 1.12632e+02, -1.88577e+03} PC: vir [ 1]={ 5.10852e+02, 5.71922e+04, 3.69013e+03} PC: vir [ 2]={-1.82055e+03, 3.43891e+03, 6.20980e+04} PC: box (3x3): PC: box [ 0]={ 9.73688e+00, 0.00000e+00, 0.00000e+00} PC: box [ 1]={ 3.24470e+00, 9.11683e+00, 0.00000e+00} PC: box [ 2]={-3.24470e+00, 4.55842e+00, 7.97596e+00} fshift after SR (27x3): fshift after SR[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} fshift after SR[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} fshift after SR[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} fshift after SR[ 3]={ nan, nan, nan} fshift after SR[ 4]={ nan, nan, nan} What am I missing? Ran Friedman wrote: > Dear all, > > I'm trying to run MD with ED sampling. The target structure is a protein > taken from one simulation, the .tpr file is taken from a different one. > I'm using a subset of the CA atoms to calculate the eigenvectors. The > problem is that the MD run crashes after set-up. > > Depending on the machine, it either crashes without any error message or > complains about "Too many iterations in routine JACOBI". > > Any suggestions? > > Thanks, > Ran. > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php