Hello,

If you want to remove constraints from TIP4P, see the standard tip4p.itp approach that replaces SETTLE with normal bonds.

#ifdef FLEXIBLE

#ifdef ORIGINAL_TIP4P

[ bonds ] ;

; i j funct length force.c.

1 2 1 0.09572 502416.0 0.09572 502416.0

1 3 1 0.09572 502416.0 0.09572 502416.0

[ angles ]

; i j k funct angle force.c.

2 1 3 1 104.52 628.02 104.52 628.02

#else

;CHARMM TIP4p

[ bonds ]

; i j funct length force.c.

1 2 1 0.09572 376560.0 0.09572 376560.0

1 3 1 0.09572 376560.0 0.09572 376560.0

[ angles ]

; i j k funct angle force.c.

2 1 3 1 104.52 460.24 104.52 460.24

#endif

I suspect the issue is more related to the force field being inadequate for a desolvated (vacuum) system, in which case you may want to minimize with dihedral or distance restraints to preserve the geometry, then perform NMA.

Thank you ...