Re: keeping a protein in a solvation box

From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Jun 13 2012 - 10:26:14 CDT

Just to followup on what has already been said, if you want to visualize
how the whole thing is working: when you look at your system, and see that
one residue poking out, look at the water on the opposite side of the box.
You should see a depression (absence of water) that matches your poking out
residue. It is those waters that your residue is interacting with during
the simulation.

~Aron

On Wed, Jun 13, 2012 at 2:17 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> Hi,****
>
> ** **
>
> If you think the moving of your protein is unnatural, it possibly come due
> to the pme. For that, there are two parameters that can remove the center
> of mass drift. One for the simulation start, to remove the com motion from
> the velocities “COMmotion” and one for during the simulation “zeromomentum”.
> ****
>
> ** **
>
> On the other hand the moving of your protein might be normal and simple
> thermodynamic. To visualize the periodic box correctly, you need to wrap
> the coordinates. I wouldn’t suggest to let namd do this, as you have no
> parameters for that, there will occur overlong bonds, as every atom that
> crosses the boundary will get wrapped. The better option is to do the
> wrapping within VMD. For that, it could look like:****
>
> ** **
>
> **1. **Load your psf and trajectory (dcd trajectory will contain
> box information)****
>
> **2. **pbc wrap –all –compound res –center com –centersel protein***
> *
>
> **3. **pbc box (draw a dynamic box)****
>
> ** **
>
> The wrapping example will wrap –all frames and does only wrap residues
> when they completely crossed the boundary (good for water to prevent long
> bond behavior) and will recenter the box around the CenterOfMass of your
> protein so the protein will not be distorted (as long as it still fits in
> the box).****
>
> ** **
>
> regards****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Aaron Oakley
> *Gesendet:* Mittwoch, 13. Juni 2012 05:27
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* Re: namd-l: keeping a protein in a solvation box****
>
> ** **
>
> On 13/06/2012, at 1:03 PM, Dr. Eddie wrote:****
>
>
>
> ****
>
> 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?****
>
> ** **
>
> The residue WILL interact with solvent, but it will be with the solvent
> molecules on the other side of the periodic system.****
>
> ** **
>
> 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.****
>
> ** **
>
> It is NOT an illusion. NAMD calculates interactions across the periodic
> boundary.****
>
> ** **
>
>
>
> ****
>
> 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--e89a8fb1fac0219b4704c25c34d0--

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