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Feature #1864

write tng files with energies

Added by David van der Spoel almost 4 years ago. Updated over 3 years ago.

Status:
New
Priority:
Normal
Category:
mdrun
Target version:
-
Difficulty:
uncategorized
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Description

It would be great if we could store the energies in the tng file.

This should be possible directly during mdrun but also in a utility reading and edr file and a trr/tng file producing a new tng file.


Related issues

Related to GROMACS - Bug #1448: multiple successive crashes during REMD can lead to .log files that do not represent the actual replica exchanges to match the .xtc files (complicating demultiplexing)New
Related to GROMACS - Bug #1667: gmx convert-tpr writes wrong number of mol in output tprNew

History

#1 Updated by Magnus Lundborg almost 4 years ago

I agree that we need to fix this. I have been planning to look into it for a long time, but other things have always come in between. One small problem is that we need to have some way to either ignore the mdrun command line -e option or allow the same file to be specified multiple times without backing it up and still writing to two different files. I'm not sure how we do that most elegantly.

#2 Updated by Mark Abraham almost 4 years ago

I think the -e and -x flags (and later, various FE and pull outputs) to mdrun are things that we should kill, writing all kinds of TNG-able data (ie everything) to TNG. So, initially we'd need some tests that mdrun writes energies now that we can read, and then update those tests to show what it can still do later. I have some machinery for energy comparisons that I'll resurrect for that.

#3 Updated by David van der Spoel almost 4 years ago

We always will need full precision energies I guess, but we can also store non-compressed x and v and f in the tng file we will not need anything else. Then -e and -x can go. That would be great.

#4 Updated by Magnus Lundborg almost 4 years ago

Indeed, energies and forces are only compressed losslessly (currently gzip is the only compressor available for lossless formats). I'm a bit hesitant about removing -e and -x for a while, though, and also even making TNG default, since there are not many programs that can open it. There is a plugin for VMD, but it's still not enabled by default. So, I think we need a temporary solution with all the current options remaining. Perhaps we could ignore the -e option if it's not explicitly set. Currently we would also require a bit of a hack to store both lossy compressed as well as losslessly compressed/uncompressed positions and velocities in the same TNG file. I guess there could be situations where that could be wanted, but I think that will have to wait.

#5 Updated by Mark Abraham over 3 years ago

  • Related to Bug #1448: multiple successive crashes during REMD can lead to .log files that do not represent the actual replica exchanges to match the .xtc files (complicating demultiplexing) added

#6 Updated by Mark Abraham over 3 years ago

  • Related to Bug #1667: gmx convert-tpr writes wrong number of mol in output tpr added

#7 Updated by Mark Abraham over 3 years ago

  • Target version deleted (5.x)

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