How to obtain the double precision coordinate file as input for the normal mode analysis

User discussions
1

I’m interested in using generating energy minimised coordinate file as input for the normal mode analysis.
However, it seems that I cannot get a gro file in the double precision format. I wonder if I can have some help, please? Thank you.
So I generate the em tpr file with
gmx_d grompp -f minim.mdp -c lig.gro -p gas.top -maxwarn 1 -o em.tpr
Then run the em.
gmx_d mdrun -o em.trr -s em.tpr
Then I tried to extract the double precision energy minimised coordinate from trr file to feed it as input for the normal mode analysis.
gmx_d trjconv -f em.trr -o em.gro -dump 99999 -s em.tpr -ndec 32
However, it seems that the em.gro has the same single precision as usual despite the -ndec 32.

Later on I was thinking of using the em.gro as input to generate the normal mode analysis.
gmx_d grompp -f nm.mdp -c em.gro -p gas.top -maxwarn 1 -o nm.tpr

Thanks.
GROMACS version: 2022
GROMACS modification: No

2

Hi,

Are you using mdrun to do normal mode analysis? Then, normal mode analysis is performed on the structure in the [tpr] file. For generating the run input file, one should use the minimized conformation from the full precision trajectory file trr, that should be possible using grompp with option -t .
I hope it works
\Alessandra

3

Thanks. This solved my problem.