On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
ah okey. Thank you.
And I have another question. Why is the protein in the corner of the box
and not in the middle?
I thought I centered it with the command:
editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470
5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut
Or not?
Have you tried trjconv -pbc mol -ur compact? The "center" of an infinite system
is an arbitrary location; you have to re-wrap the unit cell to achieve the
expected outcome. It's centered, it just may not look like it in the current
representation.
-Justin
On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I did a minimization of my structure. But the output seems a bit strange
for me, since my input was the protein with its membrane in a box like
this:
# = box P = Protein M=Membrane
#############
# PPPP #
# MPPPPM#
# PPPP #
# #
# #
#############
But the output of the minimization looks like this
#############
# PPPP#
#M MPPPP #
# PPPP #
# #
# #
##############
How can that be?
It's a triclinic representation of the unit cell. Nothing is wrong.
My box was created with:
editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470
5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut
Is a dodecahedral box appropriate for a protein in a membrane? The
inherent
symmetry of a slab of any sort dictates that you should be using a cubic
or
rectangular box. Dodecahedral and octahedral boxes are better for systems
with
spherical symmetry, like globular proteins in water.
I put solvent in it with:
genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro
2>>logErr 1>>logOut
The mdp file for the minimization looks like this:
define = -DPOSRES
integrator = steep
emtol = 10
nsteps = 1500
nstenergy = 1
energygrps = System
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
rlist = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
pbc = xyz
Can you please tell me how I can prevent my box to shift?
There is no box shift; it's just a visual representation of the
dodecahedral
box. You can "correct" it (for visualization purposes) by running trjconv
-pbc
mol -ur compact.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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.
Research Scientist
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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