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 <[EMAIL PROTECTED]> | 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
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