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 ? - Any way to prevent these large pdb files ? I did not ask for them. - How to prevent gmx executables from creating backups ? (although it is a nice thing)
The .mdp file and a part of the output is below. Thank you for the help, Maria mdp file ################################################################################################## ; minimization title = minimzation of large bilayer cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 25000 nstenergy = 1000 nstxtcout = 1000 emtol = 0.10 emstep = 0.01 nstcomm = 1 ; frequency of center of mass removal ns_type = grid ; method to update neighbour lists, "grid" is better for larger systems vdwtype = cut-off coulombtype = cut-off rlist = 1.0 ; neighbour list cutoff rcoulomb = 1.0 ; long range elec cutoff rvdw = 1.0 ; long range cutoff Tcoupl = no Pcoupl = no gen_vel = no ;pbc = no ################################################################################################### part of log ############################################################################################################ 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 #####################################################################################################################
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