Fw: [gmx-users] au--protein separate equilibration
fatemeh ramezani
fr_750 at yahoo.com
Thu Jan 17 20:49:40 CET 2013
Dear Justin thanks for your reply and,
Please help me to correct the settings of .mdp files step by step .
By these em.mdp files if I freeze only protein for the first time and after minimization I use the result .pdb file for second step of minimization that
I freeze AU atoms in it, minimization would be true?
> title = n.pdb
> cpp = /lib/cpp
> define = -DFLEXIBLE
> constraints = none
> integrator
= steep
> dt = 0.002
> nsteps = 40000
> ;constraint_algorithm = shake
> ;shake_tol = 0.0001
> ;nstenergy = 10
> ;nstxtcout = 10
> ;nstlist = 5
> ns_type = grid
> rlist = 1
> coulombtype = PME
> rcoulomb = 1
> rvdw = 1.2
> fourierspacing = 0.12
> fourier_nx
= 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 6
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Energy minimizing stuff
> emtol = 1000.0
> emstep = 0.01
> freezegrps = Protein
> freezedim = Y Y Y
> comm_mode = None
>
> 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain:
> title = n.pdb
> cpp
= /lib/cpp
> define = -DFLEXIBLE
> constraints = none
> integrator = steep
> dt = 0.002
> nsteps = 40000
> ;constraint_algorithm = shake
> ;shake_tol = 0.0001
> ;nstenergy = 10
> ;nstxtcout = 10
> ;nstlist = 5
> ns_type = grid
> rlist = 1
> coulombtype = PME
> rcoulomb
= 1
> rvdw = 1.2
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 6
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Energy minimizing stuff
> emtol = 1000.0
> emstep = 0.01
> freezegrps = AU AUI AUC
> freezedim = Y Y Y Y Y Y Y Y Y
>
comm_mode = None
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