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

[Vitaly Chaban]

> 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.


-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216