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
--
**************************************************************
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: [email protected]*
Av. do Café, s/n° * e-mail: [email protected] *
CEP: 14040-903 * Phone: +55 (16) 3602-4172 *
Ribeirão Preto, SP, Brasil * Phone: +55 (16) 3602-4222 *
**************************************************************
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