[gmx-users] Constraining N-H and H-H bonds in ammonium via SETTLE?

[John D. Chodera]

Hi all,

Can the SETTLE implementation in gromacs be used to constrain N-H and  
H-H bond lengths in ammonium (NH4+) molecules?

We have prepared an .itp file (attached below) -- based on the Pande  
group ffamber port -- for ammonium (NH4+).  If gromacs could settle N- 
H bonds too, would this involve simply adding the following line?

[ settles ]
; OW    funct    doh      dhh
1       1        0.101    0.166

Thanks!

- John

--
Dr. John D. Chodera <jchodera at gmail.com>      | Mobile    : 415.867.7384
Postdoctoral researcher, Pande lab            | Lab phone : 650.723.1097
Department of Chemistry, Stanford University  | Lab fax   : 650.724.4021
http://www.dillgroup.ucsf.edu/~jchodera
--
[ moleculetype ]
; molname       nrexcl
NH4+            3

[ atoms ]
;   nr       type  resnr    res   atom  cgnr      charge       mass
     1  amber99_39      1   NH4+     NZ     1       -0.36      14.01
     2  amber99_17      1   NH4+    HZ1     2        0.34      1.008
     3  amber99_17      1   NH4+    HZ2     3        0.34      1.008
     4  amber99_17      1   NH4+    HZ3     4        0.34      1.008
     5  amber99_17      1   NH4+    HZ4     5        0.34      1.008

[ bonds ]
;  ai    aj funct            c0            c1             
c2            c3
    1     2      1
    1     3      1
    1     4      1
    1     5      1

[ angles ]
;  ai    aj    ak funct            c0            c1            c2
c3
    2     1     3      1
    2     1     4      1
    2     1     5      1
    3     1     4      1
    3     1     5      1
    4     1     5      1