[gmx-users] Enforced rotation errors
Nash, Anthony
a.nash at ucl.ac.uk
Fri Jul 24 01:16:04 CEST 2015
Dear Carsten,
Thanks for that suggestion. Seems like that solved that particular
problem. Unfortunately though, my trajectory is not what I expected.
I have been able to rotate the cylindrical ligand about it¹s principle
axis in an earlier Œprototype¹ of my enzyme-ligand complex using iso-pf
enforced rotation. But after replacing the ligand with the Œreal¹ thing
and running a regular MD simulation for 200ns, I¹ve failed to recreate the
desired rotation using enforced rotation. I original started with iso-pf
(as it worked in the earlier case), but this resulted in lots of LINCS
errors. I then tried flex (as per my original post) and now flex-t.
I begin by calculating the moment of inertia of my cylindrical enzyme.
Using the lal01psx script for VMD I pick the 3rd vector which I add to the
.mdp file as:
rot-vec0 = 0.691585601358247 -0.6995947474399045 0.17965674311989613
It looks as though the ligand is being rotated in a big arch, rather than
rotated around its length/long axis. I take it enforced rotation, applies
the potential about this vector? My inputs 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-t ;iso-pf ;using a pivot free i.e., a
detached!:
; 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 ; <- change 100 through to 600
; 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
Any suggestions are gratefully appreciated.
Thanks
Anthony
Dr Anthony Nash
Department of Chemistry
University College London
On 20/07/2015 15:53, "Kutzner, Carsten" <ckutzne at gwdg.de> wrote:
>Dear Anthony,
>
>the problem you are experiencing with the Œflex¹ 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 Œflex-t¹ 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/pulli
>>ng/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
>
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