Hello,
just a warning concerning the last message: The mdp from gmx dump -om
will not be the complete representation of your tpr, and you will not be
able to regenerate the tpr from this mdp file! I have been working on a
variant that would make this possible, but so far have not managed it.
Cheers
Paul
On 29/11/2018 16:53, Thomas Piggot wrote:
You can get an mdp from a tpr using gmx dump -om
Cheers
Tom
On 29/11/2018 14:58, Peter Kroon wrote:
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 <jalem...@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.kr...@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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