[gmx-users] Re: error during the minimization

[gurpreet singh]

thanks for your advice Mr. Manoj
I tried the same simulation by taking a structure which was already
minimized  by another software Amber. Using that structure as the starting
structure also, i got the same error i mention earlier.
please suggest me something
thanks

On 6/29/07, M.N. Manoj <mnmanoj at gmail.com> wrote:
>
> It could be an error in protein structure ( because 1 - 9 interaction ),
> and we usually overcome similar issues by a pre -energy minimization before
> submitting to gromacs.
>
> 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
>
>
> 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
>
>
> 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
>
>
> thanks
>
>
> Gurpreet
> IIT MADRAS
>
> --
> M.N. MANOJ
> PROJECT LEADER - BIOINFORMATICS
> VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION
> BANGALORE
> INDIA
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070629/2af6c9f5/attachment.html>