[gmx-users] Re: Molecular dynamcis simualtion regarding

[Vitaly Chaban]

....Insert another protein and press ENTER...

1. Try energy minimization before MD.
2. Remove constraints temporarily.

What will be the result?

Dr. Vitaly Chaban


> On running, Molecular dynamics simulation of protein-protein complex, While
> running md run, i got this error,
> *
> "Back Off! I just backed up complex_pr1.trr to ./#complex_pr1.trr.5#
>
> Back Off! I just backed up complex_pr1.edr to ./#complex_pr1.edr.5#
>
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.011042, max 4.472447 (between atoms 12 and 14)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>
> Back Off! I just backed up step0b.pdb to ./#step0b.pdb.15#
>
> Back Off! I just backed up step0c.pdb to ./#step0c.pdb.15#
> - Show quoted text -
>
> Wrote pdb files with previous and current coordinates
>
> I used this parameter file:*
>
> define = -DPOSRES
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 10000 ; total 20.0 ps.
> nstcomm = 1
> nstxout = 250 ; collect data every 0.5 ps
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> 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
> ; Berendsen temperature coupling is on
> Tcoupl = v-rescale
> tau_t = 0.1 0.1
> tc-grps = protein non-protein
> ref_t = 300 300
> ; Pressure coupling is on
> Pcoupl = parrinello-rahman
> 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
>
> Can u help me in, how to rectify this problem and find a suitable solution
> to the problem.
>