[gmx-users] Enforced rotation errors
Kutzner, Carsten
ckutzne at gwdg.de
Fri Jul 24 10:44:21 CEST 2015
Hi Anthony,
> On 24 Jul 2015, at 01:56, Nash, Anthony <a.nash at ucl.ac.uk> wrote:
>
> After going through the literature, I think my problem lies with not
> having defined a pivot point and using what was original defined in the
> developer’s .mdp file example.
>
> I understand what a pivot point is, but I am not sure how to calculate it.
> Any suggestions would be great.
If you want the rotation group to rotate about its own axis, then use
the center of mass as the pivot, which g_traj can calculate, e.g.
The pivot will have an effect in the iso, but not in the flex potentials,
though.
Carsten
>
> Thanks
> Anthony
>
>
>
> On 24/07/2015 00:16, "Nash, Anthony" <a.nash at ucl.ac.uk> wrote:
>
>> 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/pull
>>>> i
>>>> 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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>>
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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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