[gmx-users] Snapshots in different files

[Arik Cohen]

Thanks for replaying. Indeed thats what i did with the BALL library 
which was inefficient. This led me eventually to change the library by 
adding a feature to it.

Any way thanks again

Arik

Dallas B. Warren wrote:
>
> If the time frame between snapshots is not too short, you could have 
> that as the length of each MD run, then simple extend the run to keep 
> on going.  Could be a bit inefficient.  (This is how you should run MD 
> anyway, to ensure don't lose a lot of information if the computer 
> system you are running on crashes etc.)
>
>  
>
> I wouldn't be too surprised if it was possible to hack the code so 
> that a coordinate file is spat out at some interval (even with a 
> limited index of atoms).  But that is something for those that know 
> the ins and outs of the code to tell you.
>
>  
>
> Catch ya,
>
> Dr. Dallas Warren
> Department of Pharmaceutical Biology
> Pharmacy and Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to 
> resemble a nail.
>
>  
>
> *From:* gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Arik Cohen
> *Sent:* Thursday, 8 October 2009 9:27 AM
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] Snapshots in different files
>
>  
>
> Thanks for answering.
> This would not be the case so much since another program(sniffer) can 
> be working along side gromacs
> examining each snapshot(Max 400 residues == atoms. I'm only interested 
> in the C-alpha) and then  if all criteria are met to extract/or save 
> the coor and if not to erase the snapshot.
> The aim here is to do an MD from which an ensemble of the C-alpha will 
> be created.
>
> Thanks again
>
> Arik
>
>  
>  
> Mark Abraham wrote:
>
> Arik Cohen wrote:
>
> Thanks allot, but isn't trjconv should be executed  after the 
> trajectory has finished ?. I would like to put each snapshot in a 
> different file on the fly.
>
>
> As Justin said, you can't do that. For starters, it consumes vast 
> amounts of disk. Also, it doesn't take long to do it after the fact on 
> some workstation, and it is wasteful to spend your (limited) main 
> compute resources doing I/O while post-processing output.
>
> GROMACS workflows are intended to run the simulation fast and 
> efficiently, and then allow you to process the results with the 
> various tools/filters to extract the data you need. You can even 
> post-process with mdrun -rerun if you want to get only a subset of 
> forces or something. The main exception to this principle is the use 
> of xtc-groups, IIRC.
>
> Why do you even want separate PDB frames? Visualization tools like VMD 
> will read the trajectory files.
>
> Mark
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