[gmx-users] Simulations with solvent shell
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 22 15:44:04 CEST 2009
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).
> Thanx for the VMD tip too!!
> -Aditi Borkar,
> On Tue, Sep 22, 2009 at 6:37 PM, Justin A. Lemkul <jalemkul at 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
>>> Please let me know whether these observations are acceptably normal.
>>> Thank you
>>> Aditi Borkar,
>>> Tata Institute of Fundamental Research,
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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
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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