Enforced Rotation - Fatal Error message

User discussions
1

GROMACS version: 2020.2
GROMACS modification: No
Here post your question

I have tried to use the enforced rotation approach to rotate the N-terminal Domain of the solvated protein. Then, I have received the following error message:
Fatal error:
Number of atoms in file rotref.0.trr (180116) does not match the number of
atoms in rotation group (152)!

Any suggestions? I have been used the following mdp commands:
; Enforced rotation: No or Yes
rotation = Yes
; Output frequency for angle, torque and rotation potential energy for the whole group
rot-nstrout = 10
; Output frequency for per-slab data (angles, torques and slab centers)
rot-nstsout = 10
; Number of rotation groups
rot-ngroups = 1
; Rotation group name
rot-group0 = TM_A_TM_B
; Rotation potential. Can be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2, rm2-pf, flex, flex-t, flex2, flex2-t
rot-type0 = iso-pf
; Use mass-weighting of the rotation group positions
rot-massw0 = yes
; Rotation vector, will get normalized
rot-vec0 = 0 0 1
; Rotation rate [degree/ps] and force constant [kJ/(molnm^2)]
rot-rate0 = 10.0
rot-k0 = 500.0
; Rotation rate [degree/ps] and force constant [kJ/(molnm^2)]
rot-rate0 = 10.0
rot-k0 = 500.0
; Slab distance for flexible axis rotation [nm]
rot-slab-dist0 = 1.5
; Minimum value of Gaussian function for the force to be evaluated (for flex* potentials)
rot-min-gauss0 = 0.001
; Value of additive constant epsilon’ [nm^2] for rm2* and flex2* potentials
rot-eps0 = 0.0001
; Fitting method to determine angle of rotation group (rmsd, norm, or potential)
rot-fit-method0 = norm
; For fit type ‘potential’, nr. of angles around the reference for which the pot. is evaluated
rot-potfit-nsteps0 = 21
; For fit type ‘potential’, distance in degrees between two consecutive angles
rot-potfit-step0 = 0.25

What did I do wrong here? Any suggestions?
Thank you in advance.

Masa

2

I have no experience with the option you are using, but the error is telling you that
“the reference rotref.0.trr contains all the atoms while the program is expecting to find only the rotation group”
You could try to let grompp to generate trr file for you
( see usage in http://manual.gromacs.org/documentation/current/reference-manual/special/enforced-rotation.html?highlight=usage%20 )
thus you can check what format trr should have.

3

Hi,

I would guess that you simply have some (old) rotref.0.trr lying around in the directory where you called grompp. If you have no special requirements for the rotation reference file, you can use the initial positions of the rotation group. This will be automatically done if no rotref.0.trr file is found. So deleting/moving that file from the directory where you call grompp should resolve that issue.

Best,
Carsten

4

Thank you very much for the suggestion. Yes, gromacs could not find the proper trr file, which just contains the rotational group.

5

Thank you for the suggestion. It is working now. Again, thanks.