Aditi Borkar wrote:
Dear Justin
Thank you. I was indeed using pressure coupling and I don't want to
simulate a protein in a droplet surrounded by vacuum
My protein is crescent shaped so if I use a regular simulation box, I
get one with a large volume. I hoped that using a shell will reduce
the number of atoms in the system and will facilitate computation.
Shortcuts often lead to nonsense, as you've now learned :)
So should I just stick to the traditional way of using solvent boxes
to proceed with the simulations? Is there an alternative?
Yes, you should use standard methodology, probably with a dodecahedral box.
Unfortunately you will have to deal with a larger number of atoms, but
fortunately that means your results will be meaningful, unlike what you had been
trying to do before (see Mark's post, as well).
-Justin
Thanx for the VMD tip too!!
-Aditi Borkar,
TIFR
On Tue, Sep 22, 2009 at 6:37 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
Aditi Borkar wrote:
Dear All,
I created a simulation box in editconf with -d 2.5. Then in genbox, I
used the -shell 1.4 option to define a 1.4 nm thick layer of solvent
around my protein. When I visualized the system in Rasmol, as
expected, there was a lot of "empty space" in the simulation box.
Should this vacuum create any artifacts in PBC or other energy
calculations? I did not receive any warnings or messages and so
continued with the MD simulation.
Well, you didn't receive any warnings, because as far as Gromacs is
concerned, you are doing something that is possible :)
Is your goal to simulate a protein in a droplet surrounded by vacuum?
During the MD, I saw that some ( <10) water molecules travel away from
the shell/layer around the protein and come to lie in the vacuum of
the box. Correspondingly the box size also varies depending upon the
presence of such water molecules. After about 60 ps, the box reduced
in size to just accommodate the solvent shell around the protein. And
as yet the solvent forms a layer around the protein and is not
distributed evenly in the box. By 100 ps the solvent molecules no more
form a layer but are distributed evenly within the box (cube)
I'm assuming you are using pressure coupling, so the box will deform to
accommodate the shape and size of your system. Perhaps NVT might be a more
suitable ensemble?
One last observation is that when I viewed this trajectory in VMD, the
molecule seemed to translate in space. There's no option to view the
unitcell in VMD, so I do not know whether the whole box is shifting or
just the protein+solvent is shifting inside the box.
Yes there is. Use the Tk console:
package require pbctools
pbc box
-Justin
Please let me know whether these observations are acceptably normal.
Thank you
Aditi Borkar,
Tata Institute of Fundamental Research,
Mumbai.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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