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

melichercik melichercik at nh.cas.cz
Thu Nov 29 15:04:44 CET 2018

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.


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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