[gmx-users] box size and pbc

[Wang Zhun]

Hi,
Editconf command generates a box for further solvation. When no definite box size and type are set, it will constructs a cubic box which might be the smallest to contain the solute, as far as I know.I set -d with 0.6 and full PBC for this box to simulate peptides folding.With VMD I found in one case a peptide moved out of the box while in another MD the two termini of the peptide both stretched out of the box. For the 1st one I think the PBC is ok, but what about the 2nd case if the two termini point to the opposite box sides? It seems there is no post on this editconf option. I know I'd better choose a large dodecahedron box but I just wonder if this box should be ok to perform MD with PBC.
Thanks!

[Yang Ye]

Post by Wang Zhun
Hi,
Editconf command generates a box for further solvation. When no definite box size and type are set, it will constructs a cubic box which might be the smallest to contain the solute, as far as I know.I set -d with 0.6 and full PBC for this box to simulate peptides folding.With VMD I found in one case a peptide moved out of the box while in another MD the two termini of the peptide both stretched out of the box.

Solute slowly drifting during MD is quite fine.

Post by Wang Zhun
For the 1st one I think the PBC is ok, but what about the 2nd case if the two termini point to the opposite box sides? It seems there is no post on this editconf option. I know I'd better choose a large dodecahedron box but I just wonder if this box should be ok to perform MD with PBC.
Thanks!
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[Mark Abraham]

Post by Wang Zhun
Editconf command generates a box for further solvation. When
no definite box size and type are set, it will constructs a cubic
box which might be the smallest to contain the solute, as far as I know.
I set -d with 0.6 and full PBC for this box to simulate peptides
folding. With VMD I found in one case a peptide moved out of the box
while in another MD the two termini of the peptide both stretched out
of the box.

This latter observation could be a problem. Now your termini might be
closer to the periodic copies of other termini than you would actually
want. If your termini are zwitterionic, you could be observing them
attracting each other through space. If so, neutralise each with a
counter-ion using genion.

You can also use trjconv after a simulation with the -pbc flag set
appropriately to do what you want the system to do when it's periodic.
See the manual/manpages.

Post by Wang Zhun
For the 1st one I think the PBC is ok, but what about the
2nd case if the two termini point to the opposite box sides? It seems
there is no post on this editconf option. I know I'd better choose a
large dodecahedron box but I just wonder if this box should be ok
to perform MD with PBC.

Larger is probably better, but neither cubic nor dodecahedron of
comparable size should be a problem.

Mark

[Daniela S. Mueller]

Post by Mark Abraham

Post by Wang Zhun
Editconf command generates a box for further solvation. When
no definite box size and type are set, it will constructs a cubic
box which might be the smallest to contain the solute, as far as I know.
I set -d with 0.6 and full PBC for this box to simulate peptides
folding. With VMD I found in one case a peptide moved out of the box
while in another MD the two termini of the peptide both stretched out
of the box.

This latter observation could be a problem. Now your termini might be
closer to the periodic copies of other termini than you would actually
want. If your termini are zwitterionic, you could be observing them
attracting each other through space. If so, neutralise each with a
counter-ion using genion.

if the termini interact through the periodic boundary, the box is
clearly too small. neutralising the termini is just a cosmetic solution,
and maybe you don't want to change your system like that.

Post by Mark Abraham

Post by Wang Zhun
For the 1st one I think the PBC is ok, but what about the
2nd case if the two termini point to the opposite box sides? It seems
there is no post on this editconf option. I know I'd better choose a
large dodecahedron box but I just wonder if this box should be ok
to perform MD with PBC.

Larger is probably better, but neither cubic nor dodecahedron of
comparable size should be a problem.

if your protein expands during the run, you either have to adjust the
system by increasing the box size; or if you can anticipate this, start
with a larger box to begin with.

daniela
--
Daniela S. Mueller

Diplom biologist
______________________________________________________________________

-Molecular Dynamics Group, UQ -

Address:
School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane
Australia

Phone: [phone]

Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm

**********************************************************************

- MD group, RuG -

Address:
Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Email: d.s.mueller at rug.nl

Website: http://www.rug.nl/gbb/md
______________________________________________________________________

[Mark Abraham]

Post by Daniela S. Mueller

Post by Mark Abraham

Post by Wang Zhun
Editconf command generates a box for further solvation. When
no definite box size and type are set, it will constructs a cubic
box which might be the smallest to contain the solute, as far as I

know.

Post by Wang Zhun
I set -d with 0.6 and full PBC for this box to simulate peptides
folding. With VMD I found in one case a peptide moved out of the box
while in another MD the two termini of the peptide both stretched out
of the box.

This latter observation could be a problem. Now your termini might be
closer to the periodic copies of other termini than you would actually
want. If your termini are zwitterionic, you could be observing them
attracting each other through space. If so, neutralise each with a
counter-ion using genion.

if the termini interact through the periodic boundary, the box is
clearly too small. neutralising the termini is just a cosmetic solution,
and maybe you don't want to change your system like that.

Indeed so, it is unwise to have a box so small that such an interaction
exists, however if increasing the size of the simulation box is
impractical, neutralizing the termini (either with counter-ions, or
explicitly) might be an acceptable compromise to make. After all,
isolated charges require charge separation, which requires work on the
system... that doesn't happen in biological systems without serious
machinery. Unless you know otherwise, the real system will have a
counter-ion nearby somewhere.

Post by Daniela S. Mueller

Post by Mark Abraham

Post by Wang Zhun
For the 1st one I think the PBC is ok, but what about the
2nd case if the two termini point to the opposite box sides? It seems
there is no post on this editconf option. I know I'd better choose a
large dodecahedron box but I just wonder if this box should be ok
to perform MD with PBC.

Larger is probably better, but neither cubic nor dodecahedron of
comparable size should be a problem.

if your protein expands during the run, you either have to adjust the
system by increasing the box size; or if you can anticipate this, start
with a larger box to begin with.

A normal simulation system in equilibrium won't do this... Equilibration
at constant pressure will allow the volume to adapt gradually before you
start a subsequent simulation (at constant P or V) that you care about.
This would normally be a more effective approach than guessing a size
larger than the actual system size and hoping the ensuing mess will
always sort itself out quickly into a meaningful model of reality.

Mark

[Tsjerk Wassenaar]

Hi Guys,

First off, a small correction. The default option of editconf is not a cubic
box, but a rectangular one. The use of counterions in the case of oppositely
charged ends could be a solution, but I would advice to use counterions +
physiological concentration of NaCl (0.1536M or so) to assure that there's a
proper ionic strength and there's always a proper counterion around; just
like in real life. However, it is still better to choose the box to have
such a size that the protein/peptide will fit whatever happens during the
run. If that means unfolding, the box should be large enough to contain the
stretched molecule with extra space to keep it from direct interaction over
the boundary. In addition, if the solute is free to rotate, the size should
be large enough in all directions. A good reason to use a rhombic
dodecahedron. It would be possible to use rotational constraints if the
conformational changes during the simulations aren't too dramatic.
Otherwise, you've got bad luck.

Tsjerk

--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
[phone]
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