[gmx-users] error during the minimization

[Mark Abraham]

> 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