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

[Peter Kroon]

Hi all,


thanks for all the feedback.

@Milan: I've made a tally of diskspace used per filetype in our lab. In
general people here don't save trr files at all (too expensive), yet
still out of 125TB total, 65% is made up of xtc files, and 10% is trr
files (followed by gro and xvg at 2.5% each). And that kind of backup
space becomes expensive. Of course for some simulations that were super
expensive to run we should back up the trajectories. But as a general
solution it's impossible. That also opens up the point of tiered
backups. For example: archive for the past 5 years to verify old
research results; off-site backups for the past 3 months in case the
building burns down; and local storage against accidental deletion. For
each there are different requirements and costs.

@Mark: Part of the reason for this discussion is figuring out what my
responsibility is exactly. My thought was that as the TPR in general
contains the same information as the input used to make it, at least a
partial reverse should be possible. Then again, mdp/top/itp files are
pretty small (17GB/35GB/110GB respectively) and should be very
compressible. By comparison, tprs make up 880GB here.

@Justin: Great point, thanks!


Thanks guys :)


Peter


On 29-11-18 15:29, Mark Abraham wrote:
> Hi,
>
> Yes, that's useful output, though strictly some mdp settings (like
> constraints and gen-vel) are consumed by grompp and thus not reported there.
>
> Mark
>
> On Thu, Nov 29, 2018 at 3:16 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 11/29/18 6:43 AM, 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
>> All of the input .mdp settings are also written to the header of the
>> .log file for the run.
>>
>> -Justin
>>
>>> 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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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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