[gmx-users] further discussion on the mdrun -append function

[Roland Schulz]

On Fri, Apr 6, 2012 at 12:24 AM, Peter C. Lai <pcl at uab.edu> wrote:

> Sounds like there is a lanugage barrier?
>
> Anyway, some cluster filesystems don't support append (e.g. lustre).
>

I often use append on lustre. No problem. Why do you think it doesn't work?


>
> So I never use append.
>
> I will use tpbconv -extend and -o to a *different* tpr file, then run
>

Even if you don't want to use append you don't need to use tpbconv. You can
run mdrun -wth -noappend with the total you want for nsteps. mdrun
automatically creates files called e.g. traj.part0002.trr.

Roland


> 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.
>
> Detailed Example:
>
> 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.
> >
> > Mark
>
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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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