[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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