[gmx-users] Re: Regarding Na ions

[Mark Abraham]

> Dear gmx users,
>           I am thankful to Dr.Mark and Dr.Osmair for
> their responce to my queries. As per their suggestion,
> I checked ions.itp file in that sodium atoms are
> represented by NA+ in opls force field. I am using
> gromacs 3.3.1 version.

> zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
>
> Step 32, time 0.064 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.002582 (between atoms 5262 and 5310) rms
> 0.000038
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint
> length
>    5262   5310   31.2    0.1000   0.0997      0.1000
>
> Step 33, time 0.066 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.003343 (between atoms 5262 and 5310) rms
> 0.000057
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint
> length
>    5368   5416   69.4    0.0999   0.1001      0.1000
>
> Step 34, time 0.068 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.005428 (between atoms 5262 and 5310) rms
> 0.000076
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint
> length
>    5262   5310   67.9    0.1003   0.0995      0.1000
>    5368   5416   47.0    0.1001   0.1002      0.1000
>
> Step 35, time 0.07 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.002371 (between atoms 5368 and 5416) rms
> 0.000036
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint
> length
>    5262   5310   43.4    0.0995   0.1002      0.1000
>    5368   5416   40.9    0.1002   0.0998      0.1000
> zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
>
> Can you tell where I have done mistake.
> Any suggestion is appreciated.

Please read http://wiki.gromacs.org/index.php/Blowing_Up and check that
you've followed the advice here
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation

Mark