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
>>
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>>
>
>
>
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Received on Thu Aug 27 2015 - 11:30:03 PDT
