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From: Jacob Monroe <jimonroe.umail.ucsb.edu>

Date: Mon, 31 Aug 2015 23:29:59 +0000

Hi Achim,

I see now, thank you for the clarification. I apologize for not reading your previous email more carefully. Indeed, the simulations benefited from a larger force constant for the plane-point restraint (radians are small!) and also helped me identify the bigger problem I had. Specifically, in defining my restraint to keep the peptide moving normal to the surface as it was pulled away, I defined the normal vector used in the plane-point restraint opposite to the direction of motion intended. Thus, the embarrassingly simple fix of switching the order of the three atoms defining this normal vector fixed the problem. Alternatively, attempting to fix the angle around 180 degrees instead of 0 would have worked just as well.

I’d like to clarify your later comments as well, though.

*> In my case, the steered reaction coordinate also worked well with
*

*> additional restraints, but I no longer got the distance over time for the
*

*> restrained coordinates.
*

I’m getting an output file containing the set distance along the pulling coordinate, the actual distance along this coordinate, the force at said distance, and the accumulated work. The distance seems very close to the set distance, but my force seems exceptionally noisy. I’m wondering if more than simply the force exerted by the pulling restraint is being reported in this file?

Thanks,

Jacob

*> On Aug 28, 2015, at 1:20 AM, achim.sandmann.chemie.stud.uni-erlangen.de wrote:
*

*>
*

*> Hi Jacob,
*

*>
*

*> i don't think the forces cancel each other out, but maybe the force that
*

*> keeps the peptide parallel could still be too weak, considering the
*

*> constant of 1.0 and the linear increase of the potential after 5 degrees.
*

*> Have you tried using a larger constant?
*

*>
*

*> In my case, the steered reaction coordinate also worked well with
*

*> additional restraints, but I no longer got the distance over time for the
*

*> restrained coordinates.
*

*> If that is the case for your output as well, maybe a short restart at
*

*> medium pulling distance with only the restraints and no steered reaction
*

*> coordinate could tell how much the angle in the simulation reference frame
*

*> deviates from 0. Just in case VMD uses a different definition of some
*

*> sort.
*

*>
*

*> with kind regards,
*

*> Achim
*

*>
*

*>> Hi Achim,
*

*>>
*

*>> Thanks for the suggestion! Unless I?m interpreting the implementation of
*

*>> the plane-point restraint incorrectly, I believe the forces should be
*

*>> perpendicular and thus not interfere with each other. At least, this
*

*>> should be the case if the plane-point restraint is truly enforced in an
*

*>> angular coordinate while the pulling coordinate is radial.
*

*>>
*

*>> Thanks,
*

*>> Jacob
*

*>>
*

*>>> On Aug 27, 2015, at 12:46 AM, achim.sandmann.chemie.stud.uni-erlangen.de
*

*>>> wrote:
*

*>>>
*

*>>> Hi Jacob,
*

*>>>
*

*>>> I haven't used the reaction coordinates often, I hope my suggestion
*

*>>> doesn't sound too trivial.
*

*>>> Maybe the force constant for the plane-point restraints are too weak to
*

*>>> have a significant impact on the simulation.
*

*>>>
*

*>>> Achim
*

*>>>
*

*>>>> Hi all,
*

*>>>>
*

*>>>> I am having difficulties with simulations pulling a peptide away from
*

*>>>> a
*

*>>>> surface. The surface is anchored in place with positional restraints
*

*>>>> while the peptide is pulled away from the surface with an increasing
*

*>>>> distance restraint. In order to keep the pulling coordinate roughly
*

*>>>> perpendicular to the surface, a plane-point restraint has been
*

*>>>> employed.
*

*>>>> Unfortunately, the pulling pathways seem to be quite random, with some
*

*>>>> drawing the peptide nearly parallel to the surface rather than away
*

*>>>> from
*

*>>>> it.
*

*>>>>
*

*>>>>> From the energies in the output files, it appears that all restraints
*

*>>>>> are
*

*>>>>> being imposed, so it seems that even if jar=1, other NMR restraints
*

*>>>>> can
*

*>>>>> still be applied. Additionally, the defined surface normal is
*

*>>>>> fluctuating from its starting value by no more than 2 degrees. When
*

*>>>>> drawn as a vector in VMD, the surface normal is clearly not in the
*

*>>>>> same
*

*>>>>> direction that the peptide is being pulled. The input file to sander
*

*>>>>> as
*

*>>>>> well as the definitions in the NMR restraints file for the pulling
*

*>>>>> and
*

*>>>>> plane-point restraints are provided at the end of this email.
*

*>>>>
*

*>>>> Is there a fundamental physical flaw in this type of set-up? Or is
*

*>>>> there
*

*>>>> something wrong with my implementation of the restraints in AMBER?
*

*>>>> Any
*

*>>>> suggestions would be very much appreciated!
*

*>>>>
*

*>>>> Thanks,
*

*>>>> Jacob
*

*>>>>
*

*>>>> sander input file:
*

*>>>>
*

*>>>> trajectory segment
*

*>>>> &cntrl
*

*>>>> imin = 0, nstlim = 800000, ntwr = 500,
*

*>>>> ntx = 1, irest = 0,
*

*>>>> igb = 5, gbsa = 1,
*

*>>>> saltcon = 0.000000,
*

*>>>> cut = 16.000000, surften = 0.005000,
*

*>>>> tempi = 300.000000, ntt = 3, temp0 = 300.000000,
*

*>>>> tautp = 1.000000, vrand = 500,
*

*>>>> gamma_ln = 2.000000, vlimit = 0.000000,
*

*>>>> ntc = 2, ntf = 2, tol = 1.0d-8,
*

*>>>> dt = 0.002000, nrespa = 2,
*

*>>>> ntb = 0, iwrap = 0, nscm = 510,
*

*>>>> ntpr = 500, ntave = 0,
*

*>>>> ioutfm = 0, ntwx = 500, ntwe = 500,
*

*>>>> ig = -1,
*

*>>>> jar=1,
*

*>>>> nmropt = 1,
*

*>>>> ntr = 1,
*

*>>>> restraint_wt=20.000000,
*

*>>>> restraintmask=':2-12,16,26,30,40,44,54,58,68,72,82,86,96,100-110 |
*

*>>>> (!:2-12,16,26,30,40,44,54,58,68,72,82,86,96,100-110,113-124 &
*

*>>>> .CA,C,N)',
*

*>>>> &end
*

*>>>> &wt type='DUMPFREQ', istep1=500, &end
*

*>>>> &wt type='END' &end
*

*>>>> DISANG=restraints.txt
*

*>>>> DUMPAVE=dist_force_work.dat
*

*>>>> END
*

*>>>> END
*

*>>>>
*

*>>>> restraint definitions:
*

*>>>>
*

*>>>> #Pulling
*

*>>>> &rst
*

*>>>> iat= -1, 4089,
*

*>>>> iresid=0,
*

*>>>> r2=18.0,
*

*>>>> r2a=50.0,
*

*>>>> rk2=10.0,
*

*>>>> igr1= 9, 500, 3579,
*

*>>>> &end
*

*>>>>
*

*>>>> #Point-plane angle
*

*>>>> &rst
*

*>>>> iat= 9, 500, 9, 3579 4089,
*

*>>>> iresid=0,
*

*>>>> r1=-5, r2=-2.5, r3=2.5, r4=5,
*

*>>>> rk2=1.000000, rk3=1.0000000, ialtd=0,
*

*>>>> &end
*

*>>>>
*

*>>>> _______________________________________________
*

*>>>> AMBER mailing list
*

*>>>> AMBER.ambermd.org
*

*>>>> http://lists.ambermd.org/mailman/listinfo/amber
*

*>>>>
*

*>>>
*

*>>>
*

*>>>
*

*>>> _______________________________________________
*

*>>> AMBER mailing list
*

*>>> AMBER.ambermd.org
*

*>>> http://lists.ambermd.org/mailman/listinfo/amber
*

*>>
*

*>> _______________________________________________
*

*>> AMBER mailing list
*

*>> AMBER.ambermd.org
*

*>> http://lists.ambermd.org/mailman/listinfo/amber
*

*>>
*

*>
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

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Received on Mon Aug 31 2015 - 17:00:03 PDT

Date: Mon, 31 Aug 2015 23:29:59 +0000

Hi Achim,

I see now, thank you for the clarification. I apologize for not reading your previous email more carefully. Indeed, the simulations benefited from a larger force constant for the plane-point restraint (radians are small!) and also helped me identify the bigger problem I had. Specifically, in defining my restraint to keep the peptide moving normal to the surface as it was pulled away, I defined the normal vector used in the plane-point restraint opposite to the direction of motion intended. Thus, the embarrassingly simple fix of switching the order of the three atoms defining this normal vector fixed the problem. Alternatively, attempting to fix the angle around 180 degrees instead of 0 would have worked just as well.

I’d like to clarify your later comments as well, though.

I’m getting an output file containing the set distance along the pulling coordinate, the actual distance along this coordinate, the force at said distance, and the accumulated work. The distance seems very close to the set distance, but my force seems exceptionally noisy. I’m wondering if more than simply the force exerted by the pulling restraint is being reported in this file?

Thanks,

Jacob

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Received on Mon Aug 31 2015 - 17:00:03 PDT

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