Reading double precision coordinate data with grompp

User discussions
1

GROMACS version: 2024.3 (double precision)
GROMACS modification: No

Hello there, I’m looking to couple gromacs with another code. All molecules are rigid so I need to be able to input and output atom coordinates in double precision for the other code to work.

I have complied gmx_d but I am having some trouble getting grompp to read atom position data in double precision. The file formats listed in the user manual for grompp are gro, g96, pdb, brk, ent, esp and tpr, however these do not seem to be acceptable in double precision. Is there anything I might be missing that would allow me to do this?

Any help or advice would be greatly appreciated!

Paul

2

What input (in double precision) would you like to use? Tpr files can be in double precision. You can also use the -t option to get the last coordinate frame from trr, cpt or tng files. As far as I know, those are the available options.

3

Thanks for the quick reply Magnus! I have input data for the atom coordinates (x, y, z, in double precision)

Maybe I could create a tpr file using trjconv and then use that as the structure input file for grompp?

4

If trjconv can read your input, I guess you should be able to write a trr file. I don’t think you can write a tpr file using trjconv.

5

Ah yes you’re right, sorry I was confused

I guess I am looking at this process

double precision x y z coordinates → trjconv → .trr file

.trr file → grompp with -t option → .tpr file to run MD simulation with mdrun

I’m not sure how to create compressed/binary files from my x,y,z data. Is it possible to use .pdb or .gro files with double precision in trjconv if I set -ndec to 15 or something like that?

6

I’m afraid neither pdb nor gro files will help you, since the column positions are specified in the file format. It’s possible that MDAnalysis can be useful, if your input format is supported, see 6. Coordinates modules — MDAnalysis 2.7.0 documentation.

7

That sounds like I could get it to work with MDAnalysis! Thank you for the really helpful advice!

8

g96 format contains more decimals and can be read by grompp.