Error met in pulling

User discussions
1

GROMACS version: 2023.1
GROMACS modification: Yes/No

The error I met when running mdrun:

-------------------------------------------------------
Program:     gmx mdrun, version 2023.1
Source file: src/gromacs/pulling/pull.cpp (line 668)

Fatal error:
Pull reference angle for coordinate 1 (180.000487) needs to be in the allowed
interval [0,180] deg

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Here is my mdp file, I used two CVs to pull my system:

pull                    = yes
pull_ncoords            = 2
pull_ngroups            = 6
pull-group1-name        = PULLED_RBD
pull-group2-name        = PULLED
pull-group3-name        = RBD_loc2
pull-group4-name        = RBD_loc1
pull-group5-name        = Hinge
pull-group6-name        = Rot_center
pull-group1-pbcatom     = 8050
pull-group2-pbcatom     = 32023
pull-group3-pbcatom     = 8034
pull-group4-pbcatom     = 6625
pull-group5-pbcatom     = 8497
pull-group6-pbcatom     = 15205

; Angle
pull-coord1-type        = umbrella
pull-coord1-geometry    = angle
pull-coord1-groups      = 5 1 5 6
pull-coord1-rate        = 0.25   ; deg/ps
pull-coord1-start       = yes
pull_coord1-k           = 1000

; Dihedral
pull-coord2-type        = umbrella
pull-coord2-geometry    = dihedral
pull-coord2-groups      = 3 4 4 5 5 2
pull-coord2-start       = yes
pull-coord2-rate        = 0.06  ; deg/ps
pull_coord2-k           = 1000

pull-pbc-ref-prev-step-com = yes
;

I checked the pullx.xvg and the trajectoryand I didn’t find anything strange. Can anyone provide some suggestions on how to fix or avoid this problem? Thanks!

2

BTW, I noticed that the colvar module was added in the 2024 version, can I consider running it in the 2024 version?

3

You are increasing the reference angle by 0.25 degrees per ps. I assume you run so long that the angle will go beyond 180 degrees, which is not allowed.

4

Thanks for replying!

Here is the end of my pullx.xvg file:

492.2000	60.3979	-45.7043
492.3000	60.5092	-45.4661
492.4000	60.6326	-45.457
492.5000	60.7761	-45.4257
492.6000	61.0282	-45.3097
492.7000	61.2823	-45.2352
492.8000	61.1022	-45.0466
492.9000	60.9616	-44.9462
493.0000	60.9034	-45.0955
493.1000	60.6987	-45.1402
493.2000	60.7349	-45.2171
493.3000	60.5736	-45.058
493.4000	60.5265	-45.1692
493.5000	60.2967	-45.2339
493.6000	60.5155	-45.3115
493.7000	60.6152	-45.0414
493.8000	60.6645	-44.849
493.9000	60.8

In my pullx.xvg file, I didn’t find any angle value larger than 180. The initial angle is 55.8.

5

It’s the reference angle that is the problem, not the actual angle, 55.8 + 500*0.25 is above 180.

6

Thanks! I understand this error message.

How can I solve this problem? Because I planned to pull my system Angle from about 55 degrees to 130 degrees, but my actual Angle cannot reached the target while the reference Angle has been over 180. Does this mean that I will never pull Angle to my goals?

7

I assume that your force constant is too small.