[gmx-users] Settle vs. 3 normal constraints

[Andreas Mecklenfeld]

Dear Mark,

thanks a lot for this advice - I've changed my .mdp to lincs-order = 8 
and it works just fine!

Andreas




Am 30.07.2015 um 13:59 schrieb 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
>>
>> --
>> Gromacs Users mailing list
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-- 
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