-trestart (default 10 ps) must be divisible by -dt for useful results?

User discussions
1

GROMACS version: 2024

Dear Gromacs Users:

When I run gmx msd I face this error. I can not understand what it says.

Program:     gmx msd, version 2024.3
Source file: src/gromacs/trajectoryanalysis/modules/msd.cpp (line 683)
Function:    virtual void gmx::analysismodules::Msd::analyzeFrame(int, const t_trxframe&, t_pbc*, gmx::TrajectoryAnalysisModuleData*)

Inconsistency in user input:
-trestart (default 10 ps) must be divisible by -dt for useful results.

For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/current/user-guide/run-time-errors.html

Could you please help me with that? I think this is just for the 2024 version because I did not face this error in previous versions.

2

Yes, this check (gmx msd: throw error if -trestart is not divisible by -dt and moved check for dt_ > trestart (!4259) · Merge requests · GROMACS / GROMACS · GitLab) was introduced in 2024.2 to fix this bug (Unexpected results for MSD, for various -dt (#5051) · Issues · GROMACS / GROMACS · GitLab).

Do you specify -dt? To what? What is the interval between the frames in your trajectory file?

3

Dear MagnusL,

Thanks for your reply. This a part of is my .mdp file.

; Run parameters
integrator              = md        ; leap-frog integrator
nsteps                  = 60000000     
dt                      = 0.0005     
; Output control
nstxout                 = 5000       ; save coordinates every - ps
nstvout                 = 5000       ; save velocities every - ps
nstenergy               = 5000      ; save energies every - ps
nstlog                  = 5000       ; update log file every - ps

Actually, I don’t know how to specify -dt. I know it should be in gmx msd command but I don’t know how to specify the number.

4

Then it seems like you are suffering from gmx msd crashes when trajectory was saved too often (#4694) · Issues · GROMACS / GROMACS · GitLab, which will be fixed (possibly in GROMACS 2025) by Allow femtosecond level trajectories to be analyzed in gmx-msd (!4428) · Merge requests · GROMACS / GROMACS · GitLab, but it has not been merged yet.

5

At a closer thought, it should not be that bug. Sorry. I’ll see if I can understand what’s the problem.

6

Thank you very much.

For this .mdp file :

; Run parameters
integrator              = md       
nsteps                  = 60000000 
dt                      = 0.001    
; Output control
nstxout                 = 20000    
nstvout                 = 20000    
nstenergy               = 20000    
nstlog                  = 20000

I used this command:
gmx msd -f nvt5.xtc -s nvt5.tpr -o msd.xvg -trestart 20

And, It is worked. But, I have no reason for the selection of -trestart 20 . :-))

7

In the last case it worked because -trestart must be divisible by -dt (or the time between frames. In that case you write every 20 ps, so -trestart cannot be < 20.

8

Dear MagnusL

Thanks