[gmx-users] annealing

[Luciano]

 Hi gromacs users,

 I'm with problem:

 I have a protein file generated by pdb2gmx, where the file in *.pdb
does not orginate from an X-ray structure. It was generated by Sybyl
program.

 Well, I have the following mdp file:

cpp                     = /lib/cpp
dt                      = 0.001  ; ps
nsteps                  = 100000
nstcomm                 =  1                        ; reset c.o.m. motion
nstlog                  = 100
nstlog                  = 100
nstenergy               = 100
energygrps              = system
ns_type                 = grid
coulombtype             = PME
fourierspacing          = 0.12
annealing               = yes
tinit                   = 0
ref_t                   = 1000    ; K
zero_temp_time          = 50
tcoupl                  = Berendsen
tc-grps                 = system
tau_t                   = 0.001
pcoupl                  = Berendsen
tau_p                   = 0.05
compressibility         = 4.5e-5 ; ???
ref_p                   = 1.0    ; atm
gen_vel                 = no
constraints             = none
rlist                   = 1.0
rcoulomb                = 1.0
rvdw                    = 1.0

 The grompp program generate the tpr file and when I try mdrun the
program shows:

 Getting Loaded...
Reading file octa20orig.tpr, VERSION 3.1.4 (single precision)
Reading file octa20orig.tpr, VERSION 3.1.4 (single precision)
Loaded with Money

starting mdrun 'w-gliadin'
100000 steps,    100.0 ps.

step 0Segmentation fault

 I think that was the posre.itp generated by pdb2gmx, but not have
certainty. Why the segmentation fault?!

 Cheers,

 Luciano 
 

######################################################
               Luciano Tavares da Costa
             Mestre em Engenharia Química
   icq #232852036 ; ltcosta at universiabrasil.net  
    Doutorando Laboratório de Biofisicoquímica
         Instituto de Química - USP - Brazil
             
######################################################


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