[gmx-users] Distance restraint problem with 4.0.5 version
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
Thu Oct 8 15:05:21 CEST 2009
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=
>> 0.00000000e+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.
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 = 10000
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= 1.00000001e-01, dB= 1.00000001e-01
functype[469]=CONSTR, dA= 1.08999997e-01, dB= 1.08999997e-01
functype[470]=DISRES, label= 0, type=1, low= 0.00000000e+00,
up1= 3.00000000e+00, up2= 9.39999962e+00, fac= 1.00000000e+00)
functype[471]=SETTLE, doh= 1.00000001e-01, dhh= 1.63299993e-01
fudgeQQ = 1
atomtypes:
atomtype[ 0]={radius= 0.00000e+00, volume= 0.00000e+00,
surftens=-1.00000e+00, atomnumber= 7)}
atomtype[ 1]={radius= 0.00000e+00, volume= 0.00000e+00,
surftens=-1.00000e+00, atomnumber= 1)}
--
excls[2][6..8]={0, 1, 2}
excls[3][9..9]={3}
Dis. Rest.:
nr: 3
iatoms:
0 type=470 (DISRES) 0 3
Settle:
nr: 2
iatoms:
0 type=471 (SETTLE) 0
moltype (2):
Well.... to me this does not add new information. Do you see something?
>
> 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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**************************************************************
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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