[gmx-users] Enforced rotation errors
Nash, Anthony
a.nash at ucl.ac.uk
Fri Jul 24 02:11:03 CEST 2015
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.
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
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>send a mail to gmx-users-request at gromacs.org.
>>
>>--
>>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
>>
>>--
>>Gromacs Users mailing list
>>
>>* Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>posting!
>>
>>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>* For (un)subscribe requests visit
>>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>send a mail to gmx-users-request at gromacs.org.
>
>--
>Gromacs Users mailing list
>
>* Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list