[gmx-users] further discussion on the mdrun -append function
Peter C. Lai
pcl at uab.edu
Fri Apr 6 06:24:39 CEST 2012
Sounds like there is a lanugage barrier?
Anyway, some cluster filesystems don't support append (e.g. lustre).
So I never use append.
I will use tpbconv -extend and -o to a *different* tpr file, then run
mdrun -deffnm new_extended which generates everything with the new_extended
filename prefix. Then I can trjcat or enerconv to concatenate everything
together before running the analysis.
md.mdp is configured for 1ns of simulation time
grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr
mdrun -deffnm md-1ns
-deffnm write out all files starting with this parameter: md-1ns.trr,
md-1ns.edr, md-1ns.log, etc.
Note: do not use a file extension for -deffnm or else it will put that in
the resulting filenames. If you use -deffnm md-1ns.tpr it will write out
files called md-1ns.tpr.trr md-1ns.tpr.edr etc.
tpbconv -s md-1ns.tpr -extend 2000 -o md-1ns-to-3ns.tpr
mdrun -deffnm md-1ns-to-3ns -cpi md-1ns.cpt
If you do not use -cpi here, your simulation will restart from 0, and will
be written to files beginning with "md-1ns-to-3ns"
The -cpi makes it continue from md-1ns.cpt but because of *different
filenames*, it will not append, and therefore will write new files
starting at 1ns.
trjcat -f md-1ns.trr md-1ns-to-3ns.trr -o md-to-3ns.xtc
eneconv -f md-1ns.edr md-1ns-to-3ns.edr -o md-to-3ns.edr
g_energy -f md-to-3ns.edr -o total-energy.xvg will give you a continuous
.xvg from 0 to 3ns...
If you only analysed md-1ns-to-3ns.trr/.edr then your curves will only start
from 1ns onwards.
Thus the trick is: use different file prefixes all the time and do not use
append. It is the least confusing workflow to use.
On 2012-04-06 01:56:18PM +1000, Mark Abraham wrote:
> On 6/04/2012 1:41 PM, Acoot Brett wrote:
> > Dear All,
> > Frim mdrun -h, I got the following message:
> > /-[no]append bool yes Append to previous output files when continuing
> > from checkpoint instead of adding the simulation art number to all
> > file names/
> > Thus there is the possibility that the series xvg curves can never
> > starts from 0 ns. Do you agree,
> No. If you have your initial trajectory, then I told you about both the
> available workflows yesterday. I'm going to stop repeating myself.
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Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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