Re: keeping a protein in a solvation box

From: Dr. Eddie (eackad_at_gmail.com)
Date: Tue Jun 12 2012 - 22:03:43 CDT

Thanks for the info!

Now correct me if I am wrong (and I pretty sure I am) but I can't
understand the following. If I have a piece if a protein which is sticking
out of my pbc solvated box, say residue 1, then there is no solvant for
residue 1 to interact with except the on periodic boundary and in the box.
But around residue 1 there is no solvant since it wrap (wrapWater). So it
seems it would be in vacuum but not see any surface tension of the solvant
due to the pbc. Where is my misunderstanding?

When I look at this using vmd I see part of the protein leave the box. If I
add a periodic image then it looks like the part that left the box is
solvated. But as mentioned above this seems like an illusion.

Thanks for pasting the code! I think I have a vague understanding of what
it will do. Just so I am clear, if I only have a protein in water and I
want to align my protein I need only add
protein
beneath # write your atom selection as per the user's manual
Is that correct.
Thanks very much for your help and patience!
Eddie

On Tue, Jun 12, 2012 at 6:52 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:

> 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
>>> >
>>>
>>>
>>>
>>>
>>
>

-- 
Eddie

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:38 CST