[gmx-users] error during the minimization
gps.iitm at gmail.com
Fri Jun 29 08:03:27 CEST 2007
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
> > vaccum by maintaing the restraints
> > then i added ions and water but in the very first minimization i m
> > 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
> > 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
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