[gmx-users] problem during position restraint simulation
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Aug 11 16:48:04 CEST 2009
Moutusi Manna wrote:
> Dear all,
>
> i
> want to simulate a protein solvated in water. I have downloaded the
> protein coordinate from RCSB protein data bank (ID 2KB7).
> These has 20 merged coordinate & i have taken conformer #6. Then i
> run pdb2gmx with ffG43a1 & solvate the protein with spc waters.
> Next i energy minimize the system with emtol=150.
>
> --------------------------------------------------------------------------------------------------------------
>
> Polak-Ribiere Conjugate Gradients converged to Fmax < 150 in 59 steps
>
> Potential Energy = -4.1081506e+05
>
> Maximum force = 1.3278603e+02 on atom 213
>
> Norm of force = 1.1614658e+01
>
>
>
> Performed 72 energy evaluations in total.
>
> -------------------------------------------------------------------------------------------------------------
That might be OK, but you should actually look at the structures post-EM
and during the simulation to see if they clue you in to a problem.
Also, rather than leaping straight to NPT, you can start by getting T
equilibrated with restraints at NVT, relax the restraints at NVT, and
then relax to NPT to fix the density.
Mark
> With the energy minimized structure i then run position restraint
> simulation, with fc=1000 peptide heavy atom. It gives lots of
> LINCS WARNING, wich involvs mainly backbone C O N H atoms. Then i
> have added hydrogen bond constraints & NOE distance restraints as
> given in the protein data bank and also added phi psi dihedral
> restraints. Even though i have got the LINCS WARNING involving backbone
> C O N H.
>
> ------------------my pr.mdp--------------
>
> title = sp position restraining
>
> cpp = /usr/bin/cpp
>
> define = -DPOSRES
>
> constraints = all-bonds
>
> constraint_algorithm= lincs
>
> lincs_order = 4
>
> lincs_iter = 1
>
> lincs_warnangle = 30
>
> integrator = md
>
> dt
> = 0.002 ; ps !
>
> nsteps = 250000 ; total 1 ns
>
> nstcomm = 1
>
> nstxout = 1000
>
> nstvout = 1000
>
> nstfout = 0
>
> nstlog = 1000
>
> nstenergy = 1000
>
> nstlist = 10
>
> ns_type = grid
>
> rlist = 0.9
>
> rcoulomb = 0.9
>
> vdwtype = Cut-off
>
> rvdw = 1.2
>
> fourierspacing = 0.12
>
> fourier_nx = 0
>
> fourier_ny = 0
>
> fourier_nz = 0
>
> coulombtype = PME
>
> pme_order = 4
>
> ewald_rtol = 1e-5
>
> optimize_fft = yes
>
> ;distance restraints NMR refinement
>
> disre = simple
>
> disre_weighting = equal
>
> disre_fc = 1000
>
> disre_mixed = yes
>
> disre_tau = 10
>
> nstdisreout = 5000
>
> ; dihedral restraints NMR refinement
>
> dihre = simple
>
> dihre_fc = 1000
>
> dihre_tau = 0.0
>
> nstdihreout = 5000
>
> ; Berendsen temperature coupling is on in two groups
>
> Tcoupl = berendsen
>
> tau_t
> = 0.1 0.1
>
> tc-grps = Protein SOL
>
> ref_t
> = 300 300
>
> ; Pressure coupling is on
>
> Pcoupl = berendsen
>
> tau_p = 2.0
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> pcoupltype = isotropic
>
> ; Generate velocites is on at 300 K.
>
> gen_vel = yes
>
> gen_temp = 300.0
>
> gen_seed = 173529
>
> ----------------------------------------------------------
>
> -----------in my top file i have added the following lines for distance restraints, dihedral restraints, position restraints......................................
>
>
>
> [ distance_restraints ]
>
> ; ai aj type index type' low up1 up2 fac
>
> ; HBONDS constraints
>
> 40 80 1 0 2 0.15 0.23 0.25 1.0
>
> 79 40 1 1 2 0.23 0.34 0.36 1.0
>
> .....................................................
>
> ...........................................................
>
> ; NOE
>
> 29 19 1 58 1 0.18 0.50 0.52 1.0
>
> 42 19 1 59 1 0.18 0.50 0.52 1.0
>
> 42 29 1 60 1 0.18 0.28 0.30 1.0
>
> .....................................................
>
>
> ...........................................................
>
> [ dihedral_restraints ]
>
> ; ai aj ak al type label phi dphi kfac power
>
> ;phi
>
> 7 9 11
> 16 1 1 -126.0
> 5 1 2
>
> 16 18 20 26
> 1 1 -65.5 5
> 1 2
>
> 26 28 30 39
> 1 1 -61.3 5
> 1 2
>
> .....................................................
>
>
>
> ...........................................................
>
> ; psi
>
> 1 5 7
> 9 1 1 -49.7
> 5 1 2
>
> 9 11 16 18
> 1 1 147.2 5
> 1 2
>
> .....................................................
>
>
>
>
> ...........................................................
>
> ; Include Position restraint file
>
> #ifdef POSRES
>
> #include "posre.itp"
>
> #endif
>
> --------------------------------errors in pr.log-------------------------------
>
> .....................................................
>
>
>
>
>
> .........................................................
>
> Max number of graph edges per atom is 4
>
> There are 130 distance restraints involving 136 atom pairs
>
>
>
>
>
> .........................................................
>
> There are 1 dihedral restraints involving 107 atom quartets
>
>
>
>
>
> .........................................................
>
> Step 122, time 0.244 (ps) LINCS WARNING
>
> relative constraint deviation after LINCS:
>
> max 0.992379 (between atoms 114 and 115) rms 0.042239
>
> bonds that rotated more than 30 degrees:
>
> atom 1 atom 2 angle previous, current, constraint length
>
> 114 115
> 90.0 0.1001
> 0.1992 0.1000
>
> Constraint error in algorithm Lincs at step 122
>
>
>
>
>
> .......................................................
>
>
>
> wating for suggestion to solve this problem.
>
>
>
>
>
>
>
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>
>
> ------------------------------------------------------------------------
>
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