Alexandre Suman de Araujo wrote:
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.
Hmm, the above indicates that 3.3.3 wasn't folding the function type
definitions correctly, and apparently 4.0.5 is folding the types as well
as the references to them. If you're sure you've used the same
.mdp/.top, then please submit a bugzilla (http://bugzilla.gromacs.org/)
and attach a .tar of the .top, .mdp, .tpr and .gro files.
Also have a look at grep -i disre -C 5 gmxdump4.txt to see if there's
anything interesting in the local contexts of the differences.
Mark
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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