From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon May 07 2012 - 11:05:41 CDT
Hi German:
1) add a position restraint on the CA of the C-term
2) define a distanceXY colvar and restrain it to zero
Cheers
Giacomo
On Mon, May 7, 2012 at 12:02 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> can I ask why you need either of these restrictions? The first
> restriction at the very least seems pointless. For having the CA atom
> fixed in place, I suspect your are trying to mimic AFM experiments or
> something, but physics is all relative, if you simply have the colvar be
> the distance between the C-terminal CA and the CA of the N-terminus, this
> is no different, the relative distance between the two is all that matters
> (saying one is fixed is meaningless I would think, maybe I'm missing the
> boat though).
>
> In terms of the second restriction, I can see that perhaps this is needed
> to accurately recapitulate a pulling experiment, but given the rotational
> degrees of freedom around all the residues, I don't think just pulling them
> apart along a general distance colvar will be any different than
> restricting that pulling along one axis in particular, maybe someone more
> mathematically inclined can comment.
>
> ~Aron
>
>
> On Mon, May 7, 2012 at 11:55 AM, Germán Andrés Miño <germino_at_u.uchile.cl>wrote:
>
>> Hi namd2.8 users.
>>
>> I would like to do and protein unfolding ABF calculation in an water
>> box with the following restrictions:
>>
>> CA atom of the C-terminal fixed in space.
>> CA atom of the N-terminal moving along the (0,0,Z) axis.
>>
>> I have tried with distanceZ (see below) component but my system drift
>> away from the Z axis.
>>
>> I need to minimize the size of the water box (actually a rectangle)
>> because limitations in numbers of processors and computational time
>> available.
>>
>> The colvar I am using now is:
>>
>>
>> colvarsTrajFrequency 2000
>> colvarsRestartFrequency 20000
>>
>> colvar {
>> name d
>>
>> width 0.1
>>
>> lowerboundary 50.36
>> upperboundary 380.00
>>
>> lowerwallconstant 10.0
>> upperwallconstant 10.0
>>
>> distanceZ {
>> main { atomNumbers 1921
>> }
>> ref {
>> atomNumbers 959
>> }
>> axis (0.0, 0.0, 1.0)
>>
>> }
>> }
>>
>> abf {
>> colvars d
>> fullSamples 500
>> hideJacobian
>> }
>>
>>
>> Any suggestion is truly valuated.
>> Thanks in advance.
>>
>> German Miño Galaz.
>> germino_at_u.uchile.cl
>> Postdoctoral Fellow of Grupo de Namomateriales (www.gnm.cl)
>> Departamento de Fisica
>> Universidad de Chile.
>> Palmeras 3425, Nunoa.
>> Santiago Chile
>> Tel: 0056-2-978-7439
>> Fax: 0056-2-2712973
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
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