On Thu, Oct 27, 2011 at 1:24 AM, Mo Chen <mc842.cornell.edu> wrote:
> Hi Jason,
>
> On Wed, Oct 26, 2011 at 11:52 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Wed, Oct 26, 2011 at 6:25 PM, Mo Chen <mc842.cornell.edu> wrote:
>>
>> > Dear Amber users/developers,
>> > May I ask if the direction of the random forces in SMD simulation could
>> be
>> > defined somehow?
>>
>>
>> What random forces are you talking about? The only random forces I know
>> about implemented in Amber right now are in Langevin dynamics, and that
>> has
>> nothing to do with SMD. The force induced by the moving umbrella
>> potential
>> is in no way random. It is deterministic, and analytically calculated
>> from
>> functional form of the potential (it's just a quadratic equation).
>>
>>
>> Sorry I was not phrasing it correctly, and actually I meant to say that
> the direction of the force vector is not determined at each SMD pulling step
> so that the speed is intended to be a constant, as far as I understand.
>
>
>
>> > And are all the variables listed in the example input
>> > files? Or can I use all the variables introduced in NMR &rst list? Thank
>> > you
>> > very much!
>> >
>>
>> I don't know what example input files you're looking at, but you should
>> restrict yourself to defining an umbrella potential. That is, set r1 very
>> low, to the point that the system will never sample that value or past it,
>> set r2=r3 so there's no "flat well" potential, set r4 to be very large to
>> the point that the system will never sample that value or past it, and set
>> rk2=rk3 so the potential is symmetric. Then you can define the starting
>> position of the potential and the ending position of the potential (I
>> can't
>> remember how off the top of my head, it's in the manual), and use nstlim
>> to
>> control how quickly the coordinate is changed.
>>
>> That's about the extent of the flexibility you have with SMD (but do you
>> need any more?). The main issue is calculating free energies (which is an
>> equilibrium quantity) through these non-equilibrium processes. You'll
>> need
>> the Jarzynski equation for this, and you need to satisfy the conditions of
>> this equation for a valid process.
>>
>
> I understand the theory of this. And I am trying to pull the ligand of a
> protein from one position to another by pulling one atom of the ligand from
> the initial position to the final position. So in this case I wish I could
> define the direction of the force beyond the atom to atom distance
> constraint. And I wonder if it is possible? Thank you very much!
>
Hi Jason,
Now I reconsider it and think that restraining the force direction is
probably not a good idea in this case because it limits the ligand behavior.
Though it might be nice if Amber does have this option. Thank you!
Best,
Mo
>
>
>>
>> HTH,
>> Jason
>>
>> HTH,
>> Jason
>>
>>
>> >
>> > Best,
>> > Mo Chen
>> > Graduate student
>> > Cornell University
>> > Ithaca, NY 14850
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Oct 26 2011 - 23:00:03 PDT
