Re: [gmx-users] Distance restraint problem with 4.0.5 version
Mark Abraham escreveu:
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.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[469]=DISRES, label= 1, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[470]=DISRES, label= 2, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[471]=DISRES, label= 3, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[472]=DISRES, label= 4, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[473]=DISRES, label= 5, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
.
.
.
functype[724]=DISRES, label= 256, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[725]=DISRES, label= 257, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[726]=DISRES, label= 258, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+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.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+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.
I'm submitting it in the next minutes.
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.
The result of this grep:
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= Simple
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
--
functype[465]=LJ14, c6A= 4.00489662e-03, c12A= 4.51127153e-06,
c6B= 4.00489662e-03, c12B= 4.51127153e-06
functype[466]=LJ14, c6A= 3.93701671e-03, c12A= 2.11467386e-06,
c6B= 3.93701671e-03, c12B= 2.11467386e-06
functype[467]=LJ14, c6A= 4.08602087e-03, c12A= 3.19497235e-06,
c6B= 4.08602087e-03, c12B= 3.19497235e-06
functype[468]=CONSTR, dA= 1.0001e-01, dB= 1.0001e-01
functype[469]=CONSTR, dA= 1.0897e-01, dB= 1.0897e-01
functype[470]=DISRES, label= 0, type=1, low= 0.e+00,
up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00)
functype[471]=SETTLE, doh= 1.0001e-01, dhh= 1.6323e-01
fudgeQQ = 1
atomtypes:
atomtype[ 0]={radius= 0.0e+00, volume= 0.0e+00,
surftens=-1.0e+00, atomnumber= 7)}
atomtype[ 1]={radius= 0.0e+00, volume= 0.0e+00,
surftens=-1.0e+00, atomnumber= 1)}
--
excls[2][6..8]={0, 1, 2}
excls[3][9..9]={3}
Dis. Rest.:
nr: 3
Re: [gmx-users] Distance restraint problem with 4.0.5 version
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.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[469]=DISRES, label= 1, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[470]=DISRES, label= 2, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[471]=DISRES, label= 3, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[472]=DISRES, label= 4, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[473]=DISRES, label= 5, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) . . . functype[724]=DISRES, label= 256, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[725]=DISRES, label= 257, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[726]=DISRES, label= 258, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+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.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+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 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Distance restraint problem with 4.0.5 version
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.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[469]=DISRES, label= 1, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[470]=DISRES, label= 2, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[471]=DISRES, label= 3, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[472]=DISRES, label= 4, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[473]=DISRES, label= 5, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) . . . functype[724]=DISRES, label= 256, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[725]=DISRES, label= 257, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[726]=DISRES, label= 258, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+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.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+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: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
