[gmx-users] gromacs doubt

[Justin A. Lemkul]

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 
> pre-processor

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?

-Justin

> 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
> 
> Cheers,
> Manjula Kasinathan.
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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