From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Wed Jun 17 2009 - 15:43:21 CDT
Hi Cesar, if you use the rmsd variable, instead of computing the
distance between the centers of mass of two groups of atoms, you are
computing the rmsd between: (1) the coordinates of just one group, and
(2) a set of *fixed* reference coordinates. Accordingly, the syntax
to define it is totally different from the distance.
In the example above, X meant the reference value at which Jarrod
would like to constrain the distance: no manual will ever specify it,
because that's his choice.
Metadynamics doesn't have anything to do with it either, because it's
completely different from setting up a simple harmonic restraint.
Ciao
Giacomo
---- ----
Giacomo Fiorin
Center for Molecular Modeling at
University of Pennsylvania
231 S 34th Street, Philadelphia, PA 19104-6323
phone: (+1)-215-573-4773
fax: (+1)-215-573-6233
mobile: (+1)-267-324-7676
mail: giacomo.fiorin_<at>_gmail.com
web: http://www.cmm.upenn.edu/
---- ----
On Wed, Jun 17, 2009 at 4:29 PM, Cesar Millan<pachequin_at_gmail.com> wrote:
> Hi Giacomo, i have two related questions : a) what happend if you want to
> use a rms parameter instead of distance? b) I suppose that the X value that
> you assign must be related to the metadynamics protocol, how do you assign
> this value?
>
> Thank you for your help.
>
> Cesar
>
> On Wed, Jun 17, 2009 at 1:26 PM, Giacomo Fiorin <gfiorin_at_seas.upenn.edu>
> wrote:
>>
>> Hi Jarrod, such a restraint is relatively simple to set, but you have to
>> combine several features together. You'd have to define a distance variable
>> along the z axis, and force it to the value you want.
>>
>> colvar {
>> name d
>> outputAppliedForce yes
>> outputSystemForce yes
>> distanceZ {
>> axis (0.0, 0.0, 1.0)
>> main { atomNumbers ... }
>> ref { atomNumbers ... }
>> }
>> }
>>
>> harmonic {
>> colvars d
>> centers X
>> forceConstant X
>> }
>>
>>
>>
>>
>> ---- ----
>> Giacomo Fiorin
>> Center for Molecular Modeling at
>> University of Pennsylvania
>> 231 S 34th Street, Philadelphia, PA 19104-6323
>> phone: (+1)-215-573-4773
>> fax: (+1)-215-573-6233
>> mobile: (+1)-267-324-7676
>> mail: giacomo.fiorin_<at>_gmail.com
>> web: http://www.cmm.upenn.edu/
>> ---- ----
>>
>>
>>
>> On Wed, Jun 17, 2009 at 12:07 PM, Jarrod
>> Nickel<jarrod.nickel.17_at_gmail.com> wrote:
>> > I was wondering if there are any tutorials or examples of how to use
>> > collective variables with NAMD 2.7b1. I have looked through the User's
>> > Guide
>> > and still have no idea how to set up the colvarsConfig file.
>> > Basically all I want to do is restrain the center of mass of a membrane.
>> > I
>> > am also using SMD with zero velocity on a small molecule outside the
>> > membrane. My goal is to hold the small molecule a set distance away from
>> > the
>> > membrane and measure the force on it.
>> > Any suggestions and help would be greatly appreciated.
>> >
>> > Thank you in advance,
>> > Jarrod
>> >
>>
>
>
>
> --
> ############################
> César Millán Pacheco
> Facultad de Ciencias
> Universidad Autonoma del Estado de Morelos
> Tel: 777 3297020
> Fax: 777 3207040
> email: cmp_at_uaem.mx
> pachequin_at_gmail.com
>
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