[gmx-users] forcefield and setting

[Justin Lemkul]

On 9/19/13 11:59 AM, fatemeh ramezani wrote:
>
>
>   Dear Justin
> I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for water.
>
> em.mdp file:
> title               =  n.pdb
> cpp                 =  /lib/cpp
> define              =  -DFLEXIBLE
> constraints         =  none
> integrator          =  steep
> nsteps              =  40000
> constraint_algorithm  =
> shake_tol           = 0.0001
> nstenergy           =  10
> nstxtcout           =  1
> nstlist             =  5
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1
> coulombtype         =  PME
> rcoulomb            =  1
> rvdw                =  1
> fourierspacing      =  0.12
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order           =  8
> ewald_rtol          =  1e-5
> optimize_fft        =  yes
> emtol               =  1000.0
> emstep              =  0.01
>
> md.mdp file:
> title               =  n.pdb restraining
> cpp                 =  /lib/cpp
> constraints         =  none
> integrator          =  md
> dt                  =  0.0008
> nsteps              =  25000000
> nstcomm             =  10
> comm_mode           =
> nstxout             =  250
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9
> coulombtype         =  PME
> rcoulomb            =  0.9
> rcoulomb-switch     =  1
> rvdw                =  0.5
> vdwtype             =  shift

Your van der Waals settings make no sense.  I strongly suspect that this is 
inducing very nasty artifacts.

-Justin

> ;rvdw-switch         =  0.6
> fourierspacing      =  0.12
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order           =  6
> ewald_rtol          =  1e-5
> optimize_fft        =  yes
>
>
> ; Berendsen temperature coupling is on in three groups
> Tcoupl              =  V-rescale
> tau_t               =  0.1       0.1
> tc-grps            =  Protein   Non-Protein
> ref_t               =  300       300
> ; Pressure coupling is  on
> ;Pcoupl              =  berendsen
> Pcoupl              =  no
> Pcoupltype         =  isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> energygrps          = Protein  Sol
>
>
>
> Fatemeh Ramezani
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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