[gmx-users] dummies and positional restraints

[Frauke Meyer]

Hi,

> Your atoms are dummies in the usual sense, but these are treated in
> Gromacs as any other atom, so position restraints should work.
> If you use a posre.itp file maybe you need to add the line:
> define = -DPOSRES
> to you mdp file?
> 


But it does not. I tested by running two simulations that only differ
in that the ligand consists of normal atoms in one and of dummy atoms in
the other one (atoms just differ in charge and LJ parameters).
The dummy ligand moves, the 'normal' ligand does not.
Here the RMSD of the ligand for the first steps:

RMSD of the ligand:

  0.0000      0.0000
  1.0000      0.0868
  2.0000      0.0659
  3.0000      0.1053
  4.0000      0.0800
  5.0000      0.0932
  6.0000      0.0929
  7.0000      0.0808
  8.0000      0.0903

RMSD of the dummy atoms:

  0.0000     0.0005
  1.0000     0.6156
  2.0000     0.8949
  3.0000     1.0857
  4.0000     1.2055
  5.0000     1.3212
  6.0000     1.4708
  7.0000     1.7223
  8.0000     2.0411
  9.0000     2.2720

and the topologies:

Ligand topology  
<      1          H      1    BOM     H1      1      0.398      1.008  
; qtot 0.398
<      2         OA      1    BOM     O1      1     -0.548    15.9994  
; qtot -0.15
<      3        CH2      1    BOM     C2      1       0.15     14.027  
; qtot 0
<      4        CH2      1    BOM     C4      2          0     14.027  
; qtot 0
<      5        CH2      1    BOM     C7      3          0     14.027  
; qtot 0
<      6        CH2      1    BOM    C10      4          0     14.027  
; qtot 0
<      7        CH2      1    BOM    C13      5          0     14.027  
; qtot 0
<      8        CH2      1    BOM    C16      6          0     14.027  
; qtot 0
<      9        CH2      1    BOM    C19      7          0     14.027  
; qtot 0
<     10        CH2      1    BOM    C22      8          0     14.027  
; qtot 0
<     11        CH2      1    BOM    C25      9          0     14.027  
; qtot 0
<     12        CH1      1    BOM    C28     10          0     13.019  
; qtot 0
<     13        CH1      1    BOM    C31     11          0     13.019  
; qtot 0
<     14        CH1      1    BOM    C33     12          0     13.019  
; qtot 0
<     15        CH1      1    BOM    C35     13          0     13.019  
; qtot 0
<     16        CH2      1    BOM    C37     14          0     14.027  
; qtot 0
<     17        CH2      1    BOM    C39     15          0     14.027  
; qtot 0
<     18        CH3      1    BOM    C42     16          0     15.035  
; qtot 0
---

Dummy topology
>      1        DUM      1    BOM    DUM      1        0      1.008    
; qtot 0.398
>      2        DUM      1    BOM    DUM      1        0     15.9994   
; qtot -0.15
>      3        DUM      1    BOM    DUM      1        0     14.027    
; qtot 0
>      4        DUM      1    BOM    DUM      2        0     14.027   ;
qtot 0
>      5        DUM      1    BOM    DUM      3        0     14.027   ;
qtot 0
>      6        DUM      1    BOM    DUM      4        0     14.027   ;
qtot 0
>      7        DUM      1    BOM    DUM      5        0     14.027   ;
qtot 0
>      8        DUM      1    BOM    DUM      6        0     14.027   ;
qtot 0
>      9        DUM      1    BOM    DUM      7        0     14.027   ;
qtot 0
>     10        DUM      1    BOM    DUM      8        0     14.027   ;
qtot 0
>     11        DUM      1    BOM    DUM      9        0     14.027   ;
qtot 0
>     12        DUM      1    BOM    DUM     10        0     13.019   ;
qtot 0
>     13        DUM      1    BOM    DUM     11        0     13.019   ;
qtot 0
>     14        DUM      1    BOM    DUM     12        0     13.019   ;
qtot 0
>     15        DUM      1    BOM    DUM     13        0     13.019   ;
qtot 0
>     16        DUM      1    BOM    DUM     14        0     14.027   ;
qtot 0
>     17        DUM      1    BOM    DUM     15        0     14.027   ;
qtot 0
>     18        DUM      1    BOM    DUM     16        0     15.035   ;
qtot 0



my posre.itp file:

[ position_restraints ]
;  i funct       fcx        fcy        fcz
   2    1       1000       1000       1000
  10    1       1000       1000       1000
  18    1       1000       1000       1000


Frauke

> Berk.
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