[gmx-users] Distance restraint problem with 4.0.5 version

[Alexandre Suman de Araujo]

Hi Gmxers

Some months ago I performed some simulations, with GMX 3.3.3 version, 
where I apply distance restraint between water oxygen atoms and a static 
dummy site located at the center of a sphere to keep waters inside this 
sphere. After performed an upgrade to GMX 4.0.5 version this distance 
restraint scheme stopped to work.
I read distance restraint material in 4.0.5 paper manual and I can't 
find any modification reported there.

Looking at gmxdump output from tpr's generated with grompp from 3.3.3 
and 4.0.5 versions and the same .mdp, .gro and .top files, I had this:

3.3.3 version: grep -i disre gmxdump3.txt |more

   disre                = Simple
   disre_weighting      = Conservative
   disre_mixed          = FALSE
   nstdisreout          = 100
         functype[468]=DISRES, label=   0, type=1, low= 0.00000000e+00, 
up1= 3.00000000e+00, up2= 9.39999962e+00, fac= 1.00000000e+00)
         functype[469]=DISRES, label=   1, type=1, low= 0.00000000e+00, 
up1= 3.00000000e+00, up2= 9.39999962e+00, fac= 1.00000000e+00)
         functype[470]=DISRES, label=   2, type=1, low= 0.00000000e+00, 
up1= 3.00000000e+00, up2= 9.39999962e+00, fac= 1.00000000e+00)
         functype[471]=DISRES, label=   3, type=1, low= 0.00000000e+00, 
up1= 3.00000000e+00, up2= 9.39999962e+00, fac= 1.00000000e+00)
         functype[472]=DISRES, label=   4, type=1, low= 0.00000000e+00, 
up1= 3.00000000e+00, up2= 9.39999962e+00, fac= 1.00000000e+00)
         functype[473]=DISRES, label=   5, type=1, low= 0.00000000e+00, 
up1= 3.00000000e+00, up2= 9.39999962e+00, fac= 1.00000000e+00)
         .
         .
         .
         functype[724]=DISRES, label= 256, type=1, low= 0.00000000e+00, 
up1= 3.00000000e+00, up2= 9.39999962e+00, fac= 1.00000000e+00)
         functype[725]=DISRES, label= 257, type=1, low= 0.00000000e+00, 
up1= 3.00000000e+00, up2= 9.39999962e+00, fac= 1.00000000e+00)
         functype[726]=DISRES, label= 258, type=1, low= 0.00000000e+00, 
up1= 3.00000000e+00, up2= 9.39999962e+00, fac= 1.00000000e+00)
        0 type=468 (DISRES) 389 392
        1 type=469 (DISRES) 393 396
        2 type=470 (DISRES) 397 400
        3 type=471 (DISRES) 401 404
        4 type=472 (DISRES) 405 408
        5 type=473 (DISRES) 409 412
        .
        .
        .
        256 type=724 (DISRES) 1413 1416
        257 type=725 (DISRES) 1417 1420
        258 type=726 (DISRES) 1421 1424

4.0.5 version: grep -i disre gmxdump4.txt

   disre                = Simple
   disre_weighting      = Conservative
   disre_mixed          = FALSE
   nstdisreout          = 100
         functype[470]=DISRES, label=   0, type=1, low= 0.00000000e+00, 
up1= 3.00000000e+00, up2= 9.39999962e+00, fac= 1.00000000e+00)
            0 type=470 (DISRES) 0 3


It is clear that 3.3.3 version is applying the constraints to all waters 
(what is correct) and 4.0.5 to just one. However, I can't find a way to 
fix this.

Does anyone could help me with this issue? Are there modifications in 
distance restraint algorithm in 4.0.5 version compared with 3.3.3 
version? Or this can be a bug?

Thanks

-- 
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Alexandre Suman de Araujo                                    *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto        *
Universidade de São Paulo                                    *
Dep. de Física e Química                                     *
Grupo de Física Biológica     * e-mail: asaraujo at fcfrp.usp.br*
Av. do Café, s/n°             * e-mail: ale.suman at gmail.com  *
CEP: 14040-903                * Phone: +55 (16) 3602-4172    *
Ribeirão Preto, SP, Brasil    * Phone: +55 (16) 3602-4222    *
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