[gmx-users] Running Grompp in reverse and backing up MD data

[Mark Abraham]

Hi,

On Thu, Nov 29, 2018 at 3:05 PM melichercik <melichercik at nh.cas.cz> wrote:

> Hi Peter,
> may be the gmx dump -s *.tpr can help you a little with extracting
> starting data from .tpr file. You would get all interactions, positions
> and velocities of all atoms with their types, etc., but the data about
> aminoacid sequence (well, all more complex informations that those
> mentioned above, which are needed for simulation run) you would have to
> create again (I think).
> But if you are interested - I'm producing two files during simulation:
> 1) xtc with only protein/nucleic group with more frames (there is
> directive for grompp/mdrun in .mdp file to do this),
> 2) trr with all atoms and velocities, which is more skipped (100 times
> or such).
> They are huge, sure, but not so huge, as it would be if there will be
> all in one .trr file.
>
> Cause when I wait several months for hundreds of ns to be simulated and
> if someone comes just after deleting the trajectories that he/she wants
> to calculate some other stuff from that... I don't like the idea.
>
> And now I'm just thinking about next backup layer for complete disaster
> - to backup at least skipped (from .trr) protein/nucleic parts (without
> water) with all analysis files to some external backup medium (thinking
> about Bluray - and twice, of course ;-) ).
> But I'll be happy, if someone shares better backup plan.
> Best
>

Often your institution or compute facility has backup services that you
should explore using.

Mark


> Milan
>
> On 11/29/18 12:43 PM, Peter Kroon wrote:
> > Hi Mark,
> > thanks for the rapid reply!
> > Hmmn. It doesn't have to be exactly matching input. An equivalent to
> > e.g. mdout.mdp produced by grompp would already be good enough for my
> > purposes. The same goes for a top file containing only the
> > interactions
> > relevant to the system.
> >
> > Peter
> > On 29-11-18 11:31, Mark Abraham wrote:
> >> Hi,
> >>
> >> Unfortunately there is no way to generate matching inputs to grompp
> >> from a
> >> .tpr file. In the longer term, we want that to be possible, but it
> >> will
> >> require a total rework of how users specify inputs, and that's a
> >> large
> >> effort!
> >>
> >> Mark
> >>
> >> On Thu, Nov 29, 2018 at 11:27 AM Peter Kroon <p.c.kroon at rug.nl>
> >> wrote:
> >>
> >>> Hi all,
> >>>
> >>>
> >>> In the lab we're thinking about backup solutions for MD data (and
> >>> in
> >>> particular gromacs produced data). Since trajectories tend to be
> >>> large
> >>> we quickly decided that backing up the results of simulations is a
> >>> waste
> >>> of disk space. Instead, we'll probably go for backing up the TPR
> >>> files.
> >>>
> >>> Now for the question: Is there an easy way of generating the files
> >>> used
> >>> to generate the TPR files? For example the MDP file used to make a
> >>> TPR
> >>> file? How about a top file (I assume the original split between top
> >>> and
> >>> itp is lost)? I know I can get the starting configuration (gro)
> >>> using
> >>> editconf.
> >>>
> >>> And does anyone here have any other blinding insights on backing up
> >>> MD
> >>> data?
> >>>
> >>>
> >>> Cheers,
> >>>
> >>> Peter
> >>>
> >>>
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