[gmx-users] gromacs doubt
Justin A. Lemkul
jalemkul at vt.edu
Thu May 13 13:35:33 CEST 2010
manjula kasinathan wrote:
> hi all
> i have done protein protein interaction and the complex structure
> was taken for MD simulation using Gromacs.while performing mdrun step
> for position restrain i got error. i have carried out mdrun for 1ps and
> the command given for mdrun
> and position restrain are
> grompp -f *.pdb -c *.gro -p top.top -o *.tpr
> mdrun -v -deffnm pr
> my em.mdp file
> title = com
> cpp = /usr/local/gromacs/share/gromacs/cpp ; the c
Not that this matters (since cpp is ignored in Gromacs 4.0.x and would have
caused a serious error in the 3.3.x series), but Gromacs does not distribute a
cpp, so this line is nonsense. Just FYI.
> define = -DFLEXIBLE
> constraints = none
> integrator = steep
> dt = 0.002 ; ps !
> nsteps = 3000
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = cut-off
> rvdw = 1.4
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Energy minimizing stuff
> emtol = 1000.0
> emstep = 0.01.
> here i have given nsteps 3000. but while doing energy minimization it
> considers only 1000 steps and the energy was minimized for only 1000
> steps. then i gone for position restrain step while doing Mdrun i got
> error like this
And what was the output from the energy minimization? Are the resulting
potential energy and maximum force acceptable? Have you checked the output
configuration from any unresolved clashes?
> starting mdrun 'Protein in water'
> 500 steps, 1.0 ps.
> step 400, remaining runtime: 132 s
> Step 402, time 0.804 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000119, max 0.006712 (between atoms 2873 and 2875)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 2873 2875 64.4 0.0989 0.1007 0.1000
> t = 0.868 ps: Water molecule starting at atom 93766 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> wat should i do now. how can i progress this.could any one help me plz.
> thank in advance
> Manjula Kasinathan.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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