[gmx-users] RE: g_densmap

[Ricardo Cuya Guizado]

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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