[gmx-users] PR

[Florian Dommert]

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Hello,

I haven't read the mails before, but as long as you are not in
equilibrium I do not think that PR coupling is the best way to go.
Furthermore PR is very sensitive to constraints and the time step, so
perhaps 2fs is too large. Try to perform a simulations with the
Berendsen thermostat to reach equilibrium and from there on turn on the
PR coupling. Perhaps it is also a good idea to combine Parrinello-Rahman
with the Nose-Hoover coupling scheme for the temperature as they are
very similar.

/Flo

On 11/21/2010 11:09 AM, 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
> 
> 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+
> 
> 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
> 


- -- 
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
Fax:   +49-(0)711/685-6-3658

EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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