[gmx-users] problem in npt pr for pope

[Justin A. Lemkul]

Mahnam wrote:
> 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

I can see no logical reason to use plain cutoff electrostatics, especially for a 
membrane protein system.  The artifacts are well-documented.  You should be 
using PME.  I don't know if this is the root cause of your problem, but it 
certainly won't lead to correct results.

> 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

What happens if you do not freeze your protein?  Perhaps there are unresolved 
clashes that freezing is keeping in place.

-Justin

> ; 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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