George -
I think the restraint called spherical, because there is an equal
penalty energy for the particle(s) to move in any direction. Either
the initially specified distance is decreased or increased.
Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
On Thu, Dec 13, 2012 at 1:49 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi Vitaly,
>
> Thank you for the prompt reply.
>
> I also make reference to
>
> http://enzyme.fbb.msu.ru/Tutorials/Tutorial_3/
>
> where it is stated that "So SMD method will be realized by increasing or decreasing of initial restrained distance between ligand and some active site residue during simulation. Such spherical restraint doesn't specify certain direction"
>
> My problem is that I fail to see why this restraint is spherical.
>
> Regards
>
> George
>
>
> On Dec 13, 2012, at 1:20 PM, Dr. Vitaly Chaban wrote:
>
>> Hmmm...
>>
>> Steered MD just means that you "help" your system to evolve in the
>> desired direction.
>>
>> What you are speaking about is restraints and is not steered MD in the
>> common sense. You might apply such restraints to any part of your
>> system in conventional MD simulations (for example, for more
>> convenient visualization you will not want your macromolecule to leave
>> the center of the box), but this trick will NOT make your simulations
>> steered MD by default.
>>
>> --
>> Dr. Vitaly V. Chaban
>> MEMPHYS - Center for Biomembrane Physics
>> Department of Physics, Chemistry and Pharmacy
>> University of Southern Denmark
>> Campusvej 55, 5230 Odense M, Denmark
>>
>>
>>
>>
>> On Thu, Dec 13, 2012 at 12:35 PM, George Tzotzos <gtzotzos.me.com> wrote:
>>> The Amber11 manual, in Section 4.5.2, p.108 gives an example of SMD by changing the distance between two atoms. Given that the position of the two atoms are defined by Cartesian coordinates, the push or pull between the two atoms would be directional.
>>>
>>> My understanding is (was) that SMD applies spherical restraints and therefore does not specify a certain direction.
>>>
>>> Any clarification on the directionality or non-directionality of the SMD method would be greatly appreciated.
>>
>> _______________________________________________
>> 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
Received on Thu Dec 13 2012 - 06:30:02 PST
