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

[Acoot Brett]

Thanks for the detailed explaination.
 
Will you please explain the function of "-n index.ndx " in "grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr" with some specific examples?
 
Cheers,
 
Acoot

 

________________________________
 From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, 6 April 2012 2:24 PM
Subject: Re: [gmx-users] further discussion on the mdrun -append function
  
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. 

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
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