[gmx-users] lot of pdb files written during minimization without asking for them ?

[maria goranovic]

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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