Hi,
Hopefully early in 2019 we will get to the point where the mdp inputs are
expressed as key-value data structures, perhaps in JSON. Once we do that,
that aspect of the .tpr no longer needs to be binary, and dumping it is
trivial.
Mark
On Thu, Nov 29, 2018 at 5:17 PM Thomas Piggot wrote:
>
Good to know, thanks!
Tom
On 29/11/2018 16:08, Paul bauer wrote:
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
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.
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
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).
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 wrote:
>
>
> On 11/29/18 6:43 AM, Peter Kroon wrote:
> > Hi Mark,
> >
> > thanks for the rapid
Hi,
On Thu, Nov 29, 2018 at 3:05 PM melichercik 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
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
Hi,
On Thu, Nov 29, 2018 at 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
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
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
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 wrote:
> Hi
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.
13 matches
Mail list logo
