Hi,<br><br>I am minimizing my beautiful bilayer using steepest descent. <br>- Why does gmx write out several backups of the system as pdb files ? Perhaps because it detects a crash ? <br>- Any way to prevent these large pdb files ? I did not ask for them.
<br>- How to prevent gmx executables from creating backups ? (although it is a nice thing)<br><br>The .mdp file and a part of the output is below.<br><br>Thank you for the help,<br><br>Maria<br clear="all"><br>mdp file<br>
##################################################################################################<br>; minimization<br>title = minimzation of large bilayer<br>cpp = /usr/bin/cpp<br>define = -DFLEXIBLE
<br>constraints = none<br>integrator = steep<br>nsteps = 25000<br>nstenergy = 1000<br>nstxtcout = 1000<br>emtol = 0.10<br>emstep = 0.01<br>nstcomm = 1 ; frequency of center of mass removal
<br>ns_type = grid ; method to update neighbour lists, "grid" is better for larger systems<br><br>vdwtype = cut-off<br>coulombtype = cut-off<br>rlist = 1.0 ; neighbour list cutoff
<br>rcoulomb = 1.0 ; long range elec cutoff<br>rvdw = 1.0 ; long range cutoff<br><br>Tcoupl = no<br>Pcoupl = no<br>gen_vel = no<br>;pbc = no<br>###################################################################################################
<br><br><br><br>part of log<br>############################################################################################################<br> Tolerance (Fmax) = 1.00000e-01<br> Number of steps = 25000<br>
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<br>Step= 2, Dmax= 1.2e-02 nm, Epot= 4.51389e+12 Fmax= 5.30372e+14
, atom= 1<br>Step= 3, Dmax= 1.4e-02 nm, Epot= 7.71604e+11 Fmax= 2.16386e+13, atom= 38<br>Step= 4, Dmax= 1.7e-02 nm, Epot= 4.69028e+10 Fmax= 9.92687e+11, atom= 1<br>Step= 5, Dmax= 2.1e-02 nm, Epot= 1.39383e+10 Fmax=
5.17951e+10, atom= 1<br>Step= 6, Dmax= 2.5e-02 nm, Epot= 4.34570e+09 Fmax= 2.21623e+10, atom= 1316<br>Step= 7, Dmax= 3.0e-02 nm, Epot= 2.56161e+09 Fmax= 1.88187e+10, atom= 1<br>Step= 8, Dmax= 3.6e-02 nm, Epot=
1.74047e+09 Fmax= 1.13721e+09, atom= 280<br>Step= 9, Dmax= 4.3e-02 nm, Epot= 1.63692e+08 Fmax= 1.29252e+08, atom= 1<br>Step= 10, Dmax= 5.2e-02 nm, Epot= 5.35448e+07 Fmax= 4.10206e+08, atom= 1<br>Step= 11, Dmax= 6.2e-02
nm, Epot= 4.40074e+07 Fmax= 1.66038e+07, atom= 1<br>Step= 12, Dmax= 7.4e-02 nm, Epot= 1.26246e+07 Fmax= 2.71356e+08, atom= 1<br>Wrote pdb files with previous and current coordinates<br>Step= 13, Dmax= 8.9e-02 nm, Epot=
9.09557e+06 Fmax= 8.05728e+07, atom= 1<br><br>Back Off! I just backed up step13.pdb to ./#step13.pdb.1#<br>Wrote pdb files with previous and current coordinates<br>Step= 14, Dmax= 1.1e-01 nm, Epot= 8.04910e+06 Fmax= 4.36518e+08
, atom= 1<br><br>Back Off! I just backed up step14.pdb to ./#step14.pdb.1#<br>Sorry couldn't backup step14.pdb to ./#step14.pdb.1#<br><br>Back Off! I just backed up step14.pdb to ./#step14.pdb.2#<br><br>Back Off! I just backed up
step15.pdb to ./#step15.pdb.1#<br>Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates<br><br>Back Off! I just backed up step15.pdb to ./#step15.pdb.2#<br><br>Back Off! I just backed up
step15.pdb to ./#step15.pdb.3#<br>Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates<br>Step= 15, Dmax= 1.3e-01 nm, Epot= 7.90099e+06 Fmax= 1.10680e+07, atom= 1
<br><br>Back Off! I just backed up step15.pdb to ./#step15.pdb.4#<br>Sorry couldn't backup step15.pdb to ./#step15.pdb.4#<br>Sorry couldn't backup step15.pdb to ./#step15.pdb.4#<br><br>Back Off! I just backed up step15.pdb
to ./#step15.pdb.5#<br><br>Back Off! I just backed up step16.pdb to ./#step16.pdb.1#<br>Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates<br><br>Back Off! I just backed up
step16.pdb to ./#step16.pdb.2#<br>Sorry couldn't backup step16.pdb to ./#step16.pdb.2#<br>Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates<br>Step= 16, Dmax=
1.5e-01 nm, Epot= 3.87112e+06 Fmax= 4.91035e+06, atom= 1<br>#####################################################################################################################