maria goranovic wrote:
Hi,
I am minimizing my beautiful bilayer using steepest descent.
- Why does gmx write out several backups of the system as pdb files ?
Perhaps because it detects a crash ?
As Dallas said, because they were still sitting around from your last
attempt at some calculation.
- Any way to prevent these large pdb files ? I did not ask for them.
They're indicating underlying problems. You should fix them, not the
appearance of the pdb files. :-)
- How to prevent gmx executables from creating backups ? (although it is
a nice thing)
Clean up after yourself between runs?
The .mdp file and a part of the output is below.
Output, yes...
part of log
log, no...
This is the standard error output. The log file contains different
output, and will be telling you why the PDB files are being written.
############################################################################################################
Tolerance (Fmax) = 1.00000e-01
Number of steps = 25000
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.00778e+15 Fmax= 4.91029e+17,
atom= 1315MStep= 1, Dmax= 1.0e-02 nm, Epot= 4.88043e+13 Fmax=
1.76149e+16, atom= 280
Step= 2, Dmax= 1.2e-02 nm, Epot= 4.51389e+12 Fmax= 5.30372e+14 , atom= 1
Step= 3, Dmax= 1.4e-02 nm, Epot= 7.71604e+11 Fmax= 2.16386e+13, atom= 38
Step= 4, Dmax= 1.7e-02 nm, Epot= 4.69028e+10 Fmax= 9.92687e+11, atom= 1
Step= 5, Dmax= 2.1e-02 nm, Epot= 1.39383e+10 Fmax= 5.17951e+10, atom= 1
Step= 6, Dmax= 2.5e-02 nm, Epot= 4.34570e+09 Fmax= 2.21623e+10,
atom= 1316
Step= 7, Dmax= 3.0e-02 nm, Epot= 2.56161e+09 Fmax= 1.88187e+10, atom= 1
Step= 8, Dmax= 3.6e-02 nm, Epot= 1.74047e+09 Fmax= 1.13721e+09,
atom= 280
Step= 9, Dmax= 4.3e-02 nm, Epot= 1.63692e+08 Fmax= 1.29252e+08, atom= 1
Step= 10, Dmax= 5.2e-02 nm, Epot= 5.35448e+07 Fmax= 4.10206e+08, atom= 1
Step= 11, Dmax= 6.2e-02 nm, Epot= 4.40074e+07 Fmax= 1.66038e+07, atom= 1
Step= 12, Dmax= 7.4e-02 nm, Epot= 1.26246e+07 Fmax= 2.71356e+08, atom= 1
Wrote pdb files with previous and current coordinates
Step= 13, Dmax= 8.9e-02 nm, Epot= 9.09557e+06 Fmax= 8.05728e+07, atom= 1
Back Off! I just backed up step13.pdb to ./#step13.pdb.1#
Wrote pdb files with previous and current coordinates
Step= 14, Dmax= 1.1e-01 nm, Epot= 8.04910e+06 Fmax= 4.36518e+08 , atom= 1
Back Off! I just backed up step14.pdb to ./#step14.pdb.1#
Sorry couldn't backup step14.pdb to ./#step14.pdb.1#
Back Off! I just backed up step14.pdb to ./#step14.pdb.2#
Back Off! I just backed up step15.pdb to ./#step15.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Back Off! I just backed up step15.pdb to ./#step15.pdb.2#
Back Off! I just backed up step15.pdb to ./#step15.pdb.3#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step= 15, Dmax= 1.3e-01 nm, Epot= 7.90099e+06 Fmax= 1.10680e+07, atom= 1
Back Off! I just backed up step15.pdb to ./#step15.pdb.4#
Sorry couldn't backup step15.pdb to ./#step15.pdb.4#
Sorry couldn't backup step15.pdb to ./#step15.pdb.4#
Back Off! I just backed up step15.pdb to ./#step15.pdb.5#
Back Off! I just backed up step16.pdb to ./#step16.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Back Off! I just backed up step16.pdb to ./#step16.pdb.2#
Sorry couldn't backup step16.pdb to ./#step16.pdb.2#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step= 16, Dmax= 1.5e-01 nm, Epot= 3.87112e+06 Fmax= 4.91035e+06, atom= 1
#####################################################################################################################
Mark
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