[gmx-users] Enforced rotation errors

[Kutzner, Carsten]

Dear Anthony,

the problem you are experiencing with the ‘flex’ rotation potential
could be related to the rotation group moving too far along the direction
of the rotation vector. As for V_flex, the slabs are fixed in space,
the rotation group may after some time enter a region where no reference
slab centers are defined, triggering the error that you see.

In that case, you can use the ‘flex-t’ variant of the potential. Here,
the midplane of slab n=0 is attached to the center of mass of the 
rotation group, so that the slabs move with the rotation group.
See equations 6.46 and 6.47 in the GROMACS 5.0 PDF manual.

Carsten


> On 20 Jul 2015, at 16:20, Nash, Anthony <a.nash at ucl.ac.uk> wrote:
> 
> Dear All,
> 
> I hope you can help. I am using 'flex' enforced rotation to rotate a cylindrical protein along the surface of a globular protein. Unfortunately my system is experiencing what I can only assume is an IO problem:
> 
> DD  step 949999 load imb.: force  2.9%  pme mesh/force 0.677
> 
>           Step           Time         Lambda
>         950000     1900.00000        0.00000
> 
>   Energies (kJ/mol)
>          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>    1.57412e+04    1.99606e+04    9.25263e+02    7.98071e+03    8.61345e+04
>        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>    9.59944e+05   -8.46602e+04   -6.08542e+06    6.95493e+04    1.22242e+03
>   COM Pull En.      Potential    Kinetic En.   Total Energy    Temperature
>    3.91316e+02   -5.00823e+06    8.56761e+05   -4.15147e+06    3.10369e+02
> Pres. DC (bar) Pressure (bar)   Constr. rmsd
>   -4.21942e+02    3.27704e+00    2.75540e-05
> 
> 
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 5.0.5
> Source code file: /home/columbus/chem_software/GROMACS/2015/gromacs-5.0.5/src/gromacs/pulling/pull_rotation.c, line: 2502
> 
> Fatal error:
> Enforced rotation: No reference data for first slab (n=-13), unable to proceed.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> 
> I am using gromacs 5.0.5. The .mdp settings are:
> 
> ; ENFORCED ROTATION
> ; Enforced rotation: No or Yes
> rotation                 = Yes
> ; Output frequency for angle, torque and rotation potential energy for the whole group
> rot-nstrout              = 1
> ; 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               = Collagen_CA
> ; Rotation potential. Can be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2, rm2-pf, flex, flex-t, flex2, flex2-t
> rot-type0                = flex
> ; Use mass-weighting of the rotation group positions
> rot-massw0               = yes
> ; Rotation vector, will get normalized
> rot-vec0 = 0.691585601358247 -0.6995947474399045 0.17965674311989613
> 
> ; Pivot point for the potentials iso, pm, rm, and rm2 [nm]
> ;rot-pivot0               = 4.31852e+00  1.73201e+00  1.89800e+00
> 
> ; Rotation rate [degree/ps] and force constant [kJ/(mol*nm^2)]
> rot-rate0                = 0.021
> rot-k0                   = 600.0 ; testing these
> ; Slab distance for flexible axis rotation [nm]
> rot-slab-dist0           = 1
> ; 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
> 
> The following files are being generated:
> 
> flex_1.trr
> flex_1.edr
> flex_1.log
> flex_1.xvg
> #flex_1.log.1#
> #flex_1.log.2#
> #flex_1.log.3#
> flex_1_out   <--output from the cluster
> 
> Any help is greatly appreciated.
> Kind regards
> Anthony
> 
> Dr Anthony Nash
> Department of Chemistry
> University College London
> 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa