[gmx-users] RE: g_densmap
Ricardo Cuya Guizado
rcuyag at hotmail.com
Thu May 20 20:30:04 CEST 2010
Dear Mark
I used this sequence to obtain the gro file (gro reference in the next calculations)
g_densmap_d -f tmp-prueba.gro -n index.ndx -o tmp_prueba1.gro -princ
Select a group for determining
the system size:
Group 0 (
System) has 6370 elements
Group 1 (
HEME) has 47 elements
Group 2 (
SOL) has 6321 elements
Group 3 (
NA+) has 2 elements
Group 4 ( NA) has 1 elements
Group 5 ( NC) has 1 elements
Group 6 (
CHB) has 1 elements
Group 7 (
CHD) has 1 elements
Group 8 (
CHB-CHD) has 2 elements
Group 9
( Carb_ring) has 4 elements
Group 10 (
CHC) has 1 elements
Group 11 (
CHA) has 1 elements
Group 12 (
nitrog) has 3 elements
Group 13 (
ow_teste) has 1 elements
Group 14 (
HW1_HW2) has 4214 elements
Group 15 ( OW) has 2107 elements
Group 16 ( Fe) has 1 elements
Select a group: 0
Selected 0: 'System'
system size : 5.486
5.648 6.394 (nm)
center
: 3.463 3.499
1.671 (nm)
box vectors : 4.471
4.471 4.563 (nm)
box angles
: 60.66 60.66
90.00 (degrees)
box volume
: 65.78 (nm^3)
Select group for the
determining the orientation
Group 0 (
System) has 6370 elements
Group 1 (
HEME) has 47 elements
Group 2 (
SOL) has 6321 elements
Group 3 (
NA+) has 2 elements
Group 4 ( NA) has 1 elements
Group 5 ( NC) has 1 elements
Group 6 (
CHB) has 1 elements
Group 7 (
CHD) has 1 elements
Group 8 (
CHB-CHD) has 2 elements
Group 9 (
Carb_ring) has 4 elements
Group 10 (
CHC) has 1 elements
Group 11 (
CHA) has 1 elements
Group 12 (
nitrog) has 3 elements
Group 13 (
ow_teste) has 1 elements
Group 14 (
HW1_HW2) has 4214 elements
Group 15 ( OW) has 2107 elements
Group 16 ( Fe) has 1 elements
Select a group: 8
Selected 8: 'CHB-CHD'
new system size : 5.486
5.648 6.394
shift
: -0.110 -0.145 -0.026 (nm)
new center :
3.353 3.353 1.645 (nm)
new box vectors : 4.471
4.471 4.563 (nm)
new box angles :
60.66 60.66 90.00 (degrees)
new box volume :
65.78 (nm^3)
Select a group for output:
Group 0 (
System) has 6370 elements
Group 1 (
HEME) has 47 elements
Group 2 (
SOL) has 6321 elements
Group 3 (
NA+) has 2 elements
Group 4 ( NA) has 1 elements
Group 5 ( NC) has 1 elements
Group 6 (
CHB) has 1 elements
Group 7 (
CHD) has 1 elements
Group 8 (
CHB-CHD) has 2 elements
Group 9 (
Carb_ring) has 4 elements
Group 10 (
CHC) has 1 elements
Group 11 (
CHA) has 1 elements
Group 12 (
nitrog) has 3 elements
Group 13 (
ow_teste) has 1 elements
Group 14 (
HW1_HW2) has 4214 elements
Group 15 ( OW) has 2107 elements
Group 16 ( Fe) has 1 elements
Select a group: 0
Selected 0: 'System'
where CHB-CHD (molecular axis) must to coincide with the axis (X or Y).
My molecule is well centered and the box axis coincide with the molecular axis (chosen according to my interest)
The results are similar to make it in two steps
(1) g_densmap_d -f tmp-prueba.gro -n index.ndx -o tmp_prueba1.gro -princ(2) g_densmap_d -f tmp-prueba1.gro -n index.ndx -o tmp_prueba2.gro -c
The molecule was centered in every step simulation.
trjconv_mpi_d -s heme_centered.tpr -f dm10nsheme.xtc -o dm10nsheme_cent.xtc -center -boxcenter rect -pbc mol
The box was rotate to XY plane concide with the XY molecular plane in every step simulation
trjconv_mpi_d -s tmp_prueba2.gro -f dm10nsheme_cent.xtc -o dm10nsppix_cent_norotTrans.xtc -fit rot+trans
To obtain the XY density map
g_densmap_mpi_d -f m10nsppix_cent_norotTrans.xtc -s tmp_prueba2.gro -n index.ndx -o tmpdensmaphemeXY.xpm
when I applied the g_densmap tool, there is not difference with my previous result. In the density map, my molecule appear in the corner, and white diffuse regions (maybe by the box rotations) appear.
I think the problem will be the way that I eliminate the rotations and translations.
But I don't have a clear idea of what I've done wrong
Regards
Ricardo
..............................................................................................................................
Please use a descriptive
subject line to help everybody.
I suspect your use editconf
is your problem. -princ may not preserve your box the way you've assumed. Try
-princ -c, or editconf -princ then editconf -c.
It's also pointless and
error-prone to compile MPI versions of the GROMACS tools. Only mdrun is
MPI-aware, and the installation guides make this clear.
Mark ............................................................................................................................
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