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

[Peter C. Lai]

I sometimes use non-standard index groups in my .mdp. If you only reference
the moleculetypes and/or Protein or Non-protein in your .mdp then you don't
need a special index.ndx and the -n option becomes optional.

Example:
I specialize in membrane proteins.

In my .mdp I have:

tc-grps         = Protein POPC Water_and_ions_Ligands

Water_and_ions_Ligands is not a standard index group, I have to construct it
using make_ndx, so I need to tell grompp where to find the explicit index
file.

Example (from Justin's tutorial)

tc-grps = Protein Non-Protein

Then I do not need to use -n in grompp because these standard groups are 
implicit.

You can get a list of implicit standard groups for your system by running
make_ndx on your .gro file. Control-C to exit without writing a file.


On 2012-04-05 09:51:58PM -0700, Acoot Brett wrote:
> 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
> Genetics, Div. of Research    | 705 South 20th Street
> pcl at uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
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> 
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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			|
==================================================================