[gmx-users] PR

[Mark Abraham]

On 21/11/2010 9:09 PM, pawan raghav wrote:
> Thank mark for comments, but I have check the structure after energy 
> minimization through ramachandran plot and found 82% residues were 
> lies in core region. After performed position restrained dynamics it 
> reduced to 52% in core region also 1 bad contact was found. I have 
> taken SPC water model then add 2 NA+ ions in the solvent, done energy 
> minimization at emtol value of 2000 kJ/mol and steps for 250. Below is 
> the pr.mdp file for position restraiuned dynamics, please let me know 
> if any serious flaws. So help me by giving me the reference.
>
> title = Position restrained of Bcl-2.
>
> integrator = md
>
> define = -DPOSRES
>
> dt = 0.002
>

A smaller timestep during equilibration will better help the integration 
cope with anything that is not very happy.

> nsteps = 100000
>
> nstcomm = 1
>
> nstxout = 250
>
> nstvout = 1000
>
> nstfout = 0
>
> nstlog = 10
>
> nstenergy = 10
>
> nstlist = 5
>
> xtc_grps = protein sol
>
> energygrps = protein sol
>
> ns_type = grid
>
> rlist = 1.0
>
> coulombtype = PME
>
> rcoulomb = 1.0
>
> vdwtype = cut-off
>
> rvdw = 1.4
>
> fourierspacing = 0.135
>
> fourier_nx = 0
>
> fourier_ny = 0
>
> fourier_nz = 0
>
> pme_order = 4
>
> ewald_rtol = 1e-5
>
> optimize_fft = yes
>
> Dispcorr = no
>
> Tcoupl = v-rescale
>
> tc-grps = protein sol NA+
>

Those groups are bad. See 
http://www.gromacs.org/Documentation/Terminology/Thermostats

Mark

> tau_t = 0.1 0.1 0.1
>
> ref_t = 300 300 300
>
> Pcoupl = parrinello-rahman
>
> Pcoupltype = isotropic
>
> tau_p = 0.5
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> gen_vel = yes
>
> gen_temp = 300.0
>
> gen_seed = 173529
>
> constraints = all-bonds
>
>
>
> -- 
> Pawan