[gmx-users] g_densmap

[Ricardo Cuya Guizado]

Dear Friends
 When I applied the g_densmap to my system, my molecule appear in the corner of the xpm file and white diffuse regions (maybe by the box rotations) appear.I used this sequence to obtain the gro file (gro reference used for rotate the box to coincide with the XY molecular plane. The molecule was previously centered).

(to make the XY molecular plane coincide with the XY of the box, the group 9 lies on the XY molecular plane)
 editconf_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: 9
 Selected 9: 'Carb_ring '

 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'

 * My molecule is well centered and the box axis coincide with the
 molecular axis (chosen according to my interest)


 *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


 *In every simulation step the box was rotate to XY plane to concide with the XY molecular plane in
 every step simulation, in this step i used the previously tmp_prueba1.gro)

 trjconv_mpi_d -s tmp_prueba1.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_prueba1.gro -n
 index.ndx -o tmpdensmaphemeXY.xpm





 Regards

 Ricardo Cuya
 PUC-Rio, Brasil 		 	   		  
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