[gmx-users] Re: water dimer is gas phase

[Justin A. Lemkul]

Vitaly Chaban wrote:
>> the equlibration file I used
>>
>> title               =  cpeptid position restraining
>> cpp                 =  /usr/bin/cpp
>> constraints         =  none
>> integrator          =  md
>> dt                  =  0.001    ; ps !
>> nsteps              =  1000000      ; total 1.0 ps.
>> nstcomm             =  1
>> nstxout             =  10000
>> nstvout             =  10000
>> nstfout             =  0
>> nstlog              =  10
>> nstenergy           =  10
>> nstlist             =  10
>> ns_type             =  simple
>> comm_mode           = none
>> coulombtype         = cut-off
>> vdwtype             = cut-off
>> rlist               =  0.0
>> rcoulomb            =  0.0
>> rvdw                =  0.0
>> pbc                 =  no
>> fourierspacing      = 0.12
>> fourier_nx               = 0
>> fourier_ny               = 0
>> fourier_nz               = 0
>> pme_order           = 4
>> ewald_rtol          = 1e-5
>> optimize_fft        = yes
>> ; Berendsen temperature coupling is on
>> Tcoupl = nose-hoover
>> tau_t = 0.1
>> tc-grps  =system
>> ref_t =   298
>> ; Pressure coupling is  on
>> Pcoupl              = NO ;Parrinello-Rahman
>> pcoupltype          = isotropic
>> tau_p               =  2.0
>> compressibility     =  4.5e-5
>> ref_p               =  1.0
>> ; Generate velocites is on at 300 K.
>> gen_vel             =  yes
>> gen_temp            =  298.0
>> gen_seed            =  173529
>>
>> Is ther any thing wrong with my mdp files.
>> WHy they is so much change is cooridnates in the .pdb file.
>>
> 
> 
> 
>  Nilesh:
> 
> Set periodic conditions. This will restrict the coordinates to small numbers.
> 
> 

For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct to 
obtain a gas-phase system.  The system has clearly exploded.  To diagnose, I 
would suggest:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

-- 
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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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