Hi Jacob,
no need to apologize at all, I'm happy to hear that yu could solve the
problem.
As for the files, I use restraints to keep DNA ends from unwinding. The
NMR-restraint outputfile lists the restrained distances over time like
this:
0 1.759 1.781 1.916 1.965
500 1.640 1.801 2.032 1.823
1000 1.682 1.796 1.843 1.879
1500 1.733 1.753 1.845 1.848
2000 1.731 1.679 1.902 1.888
2500 1.706 1.768 2.086 1.933
3000 1.640 1.783 1.755 1.794
3500 1.741 1.766 1.855 1.873
4000 1.707 1.815 2.049 1.834
4500 1.748 1.792 1.936 1.905
...
When an SMD reaction coordinate is set, it uses the same input file as the
NMR-restraints and is also given the same output-file name. This output
file name contains the same parameters that you described:
31.19480 31.19015 46.53047 0.00000
31.19580 31.18994 58.57011 0.05255
31.19680 31.18970 71.00753 0.11734
31.19780 31.18931 84.86008 0.19527
31.19880 31.18897 98.34580 0.28688
31.19980 31.18898 108.23863 0.39017
31.20080 31.18934 114.60081 0.50159
...
It however doesn't contain the NMR-restrained distances, which I think is
intentional, since there is only one specified output file and the SMD
parameters are more important.
Since the forces of the NMR restraints were not listet in this file before
(only in the .out file), and I didn't notice qualitative differences
between SMD calcs with and without NMR-restraints, I work under the
assumption that the NMR-restrained distances are completely omitted and
not somehow uncluded within the SMD reaction coordinate output.
If anybody knows this to be false I would be thankful if you would tell me.
Since you don't use explicit solvent and the intendet and actual reaction
coordinate are close, I don't know what could cause the noise in the
pulling force.
with kind regards,
Achim
> 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
>>>>>
>>>>
>>>>
>>>>
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>>
>>
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Received on Tue Sep 01 2015 - 06:00:04 PDT
