[gmx-users] problem in npt pr for pope

[Mahnam]

In God We Trust
Hello everyone 
We have a problem for equilibrate the system with a protein within 
POPE. we have searched mailing list , we dident any good note. We have used 
pope.pdb from Dr. Tielemans website. We have inserted our protein into pope 
and minimized it and equilibrated it with NVT ensemble for 2 ns, and 
temperture was stable, but when we want to equilibrate our system 
with NPT ensemble it dosen't accept lincs algoritm and says :
" presure coupling more than 1% " and also " box was shifted at least 10 
time. 
here is our npt file for position reastrant:
constraints         =  all-bonds
define              =  -DPOSRES  -DPOSRES_pop
integrator          =  md
dt                  =  0.002; ps 
nsteps              =  2500000; .
nstcomm             =  1
comm_mode           =  Linear
comm_grps           =  upper lower SOL
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  1
ns_type             =  grid
rlist               =  1
coulombtype         =  cut-off
rcoulomb            =  1.4
rvdw                =  1.4
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes
niter               = 20
pbc                 = xyz 
nstcgsteep               = 1000
nbfgscorr                = 10
vdwtype             = cut-off
DispCorr            =  EnerPres
freezegrps           = Protein
freezedim            = Y Y Y
emtol                = 100
emstep               = 0.01
energygrps          = Protein 
energygrp_excl      = Protein  Protein
; Berendsen temperature coupling is on in three groups
Tcoupl              =  Nose-Hoover
tau_t               =  0.1  0.1  0.1       
tc-grps      =  Protein  POP  bulk   
ref_t               =  100    100   100        
; Pressure coupling is  on
Pcoupl              =  Berendsen 
Pcoupltype          =  semiisotropic
tau_p               =  1  1  
compressibility     =  4.5e-05  4.5e-05  
ref_p               =  1   1  
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  100.0
gen_seed            =  173529
constraint-algorithm =lincs 
lincs_iter          = 1
lincs_order         = 4

whould you please gide me

Many thanks in advance for your help and your reply.
Yours truly 
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 13145-1384
Tehran 
Iran 
http://www.ibb.ut.ac.ir/
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