From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jun 12 2012 - 18:52:05 CDT
And at any rate, Eddie, your protein *never* leaves the box, for as long as
you have PBCs enabled. Most of the time you're sure of that, if you want
to be 100% sure look into using VMD to wrap the coordinates.
On Tue, Jun 12, 2012 at 7:50 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
> Thanks Aaron! You beat me to this.
>
> However, I can see another email coming requesting to clarify, so I'm
> pasting here the example configuration. The last time I sent this to
> namd-l was a while ago and may not show up easily in a keyword search.
>
> colvar {
>
> name com
> width 1.0
>
> distance {
> group1 {
> # write your atom selection as per the user's manual
> }
> group2 {
> # change the position of this dummyAtom if you want a different
> # point as the center
> dummyAtom (0.0, 0.0, 0.0)
> }
> }
> }
>
>
> colvar {
>
> name orient
> width 0.05
>
> orientation {
> atoms {
> # write your atom selection as per the user's manual
> }
> refPositionsFile reference_coordinates.pdb
> }
> }
>
>
> harmonic {
> colvars com orient
> forceConstant 10.0
> centers 0.0 (1.0, 0.0, 0.0, 0.0)
> }
>
>
> On Tue, Jun 12, 2012 at 7:45 PM, Aaron Oakley <aarono_at_uow.edu.au> wrote:
>
>> You could use collective variables to remove the rotation/translation
>> component of your macromolecule.
>>
>> a++
>>
>> On 13/06/2012, at 8:44 AM, Dr. Eddie wrote:
>>
>> > Hi all,
>> > What is the best way to keep a protein inside a solvation box?
>> >
>> > With wrapwater and wrapall on my protein still climbs out of the box
>> (presumably still experiencing solvation due to periodic boundary
>> conditions, but I can't be sure). I'd like the protein to stay in the box.
>> Should I fix one single atom in the protein? Is there a better way than
>> just making an enormous box?
>> > Thanks,
>> > Eddie
>> >
>>
>>
>>
>>
>
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