[gmx-users] Settle vs. 3 normal constraints

[Mark Abraham]

Hi,

Using "normal" constraint algorithms with triangles of constraints can be
tricky with some integrators. Do check out the several manual sections that
talk about how these algorithms work, e.g. you may need to increase
lincs-order

Mark

On Wed, Jul 29, 2015 at 5:47 PM Andreas Mecklenfeld <
a.mecklenfeld at tu-braunschweig.de> wrote:

> Dear GROMACS users,
>
> I want to calculate the solvation free energy of a rigid water molecule,
> e.g. TIP4P-Ew.
> To do this, I define one solute molecule which I refer to as
> couple-moltype in the .mdp-file (SOL).
> The solvens molecules are exactly the same, just named differently for
> distinction (SOLB).
>
> Since I can't simulate two molecule types with settle, I want to use
> constraints. My .itp-file looks like this:
>
>
> ----------------------------------------------------------------------------------------------------
>
> ;
> ; tip4pew Water model
> ;
> [ moleculetype ]
> ; molname    nrexcl
> SOL        2
>
> [ atoms ]
> ; id  at type     res nr  res name  at name  cg nr  charge    mass
>    1   OW_tip4pew  1       SOL       OW       1       0 16.00000
>    2   HW_tip4pew  1       SOL       HW1      1       0.52422 1.00800
>    3   HW_tip4pew  1       SOL       HW2      1       0.52422 1.00800
>    4   MW                1       SOL       MW       1      -1.04844 0.00000
>
>
>
> [ constraints ]
> 1    2    1    0.09572    ; func. 1: chemical bond (O-H)
> 1    3    1    0.09572    ; func. 1: chemical bond (O-H)
> 2    3    2    0.15139    ; func. 2: no chemical bond (H-H)
>
>
>
> [ virtual_sites3 ]
> ; Vsite  from              funct   a               b
> 4       1       2       3       1       0.106676721     0.106676721
>
>
> [ exclusions ]
> 1    2    3    4
> 2    1    3    4
> 3    1    2    4
> 4    1    2    3
>
>
> ; The position of the virtual site is computed as follows:
> ;
> ;          O
> ;
> ;          V
> ;
> ;    H        H
> ;
> ; Ewald tip4p:
> ; const = distance (OV) / [ cos (angle(VOH))     * distance (OH) ]
> ;      0.0125 nm    / [ cos (52.26 deg)    * 0.09572 nm    ]
> ;    then a = b = 0.5 * const = 0.106676721
> ;
> ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
>
>
> ----------------------------------------------------------------------------------------------------
>
> The temperature derivates by 20 K using the sd-intergrator as thermostat.
> By using the settle algorithm for only one molecule (same .mdp and .gro
> files as for the constrained), I gain results as expected.
>
> I'm sorry if this is a trivial question.
>
> Thanks for your support!
> Andreas
>
>
> --
> M. Sc. Andreas Mecklenfeld
> Stipendiat
>
> Technische Universität Braunschweig
> Institut für Thermodynamik
> Hans-Sommer-Straße 5
> 38106 Braunschweig
> Deutschland / Germany
>
> Tel: +49 (0)531 391-2634
> Fax: +49 (0)531 391-7814
>
> http://www.ift-bs.de
>
> --
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