[gmx-users] error during the minimization

[gurpreet singh]

Sorry
 I will take care of this  in the future.
Thanks  for your advice .

On 6/29/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
>
> > i m carryin a protein explicit solvent simulation  using gromacs  3.3
> > for intially minimizing the hydrogen i did some small mini and equi in
> the
> > vaccum by maintaing the restraints
> > then i added ions and water but in the very first minimization i m
> getting
> > the following error
>
> Please use normal capitalization and punctuation and do not invent your
> own abbreviations and shorthands. You're trying to communicate with busy
> people whose advice you want for free. To improve your chances of getting
> useful help, you should make things easy for them, not easy for yourself.
>
> If you were still using restraints in this second minimization, try taking
> them off for a second vacuum geometry optimization phase.
>
> > 1-4 interaction between 1 and 9 at distance 8.454 which is larger than
> the
> > 1-4 table size 1.000 nm
> > These are ignored for the rest of the simulation
> > This usually means your system is exploding,
> >
> >
> > in the log file im geting :
> >
> > 4 inconsistant shifts check ur topology
> >
> > following is my input file :
> >
> > title               = 1min in water
> > define              = -DPOSRES
> > integrator          = steep
> > dt                  = 0.001
> > constraints         = none
> > nsteps              = 500
> > nstlist             = 10
> > rcoulomb            = 1
> > rlist               = 1
> > rvdw                = 1.4
> > ns_type             = grid
> > coulombtype         = PME
> > pbc                 = xyz
> > gen_vel             = no
> > fourierspacing      = 0.12
> > pme_order           = 6
> > ewald_rtol          = 1e-5
> > optimize_fft        = yes
> > comm_mode           = angular
> > emtol               = 100.0
> > emstep              = 0.01
>
> This seems fine.
>
> > after adding the ions i have modified the topology file,
> > plz tel me what is the exact reason for this error or what are
> the  other
> > things i should check in relation to the  error
>
> Mark
>
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