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

[Mark Abraham]

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