[gmx-users] Re: using previous window restart file

[gromacs query]

Dear All,

Please any suggestion?

regards,


On Mon, Jun 3, 2013 at 4:53 PM, gromacs query <gromacsquery at gmail.com>wrote:

> Dear All,
>
> (Sorry for long mail!)
>
> (Thanks Thomas Schlesier for clarifying previous umbrella queries)
>
> I wish to run umbrella samplings using restart file of previous window.
> e.g. initial distance between A (reference) and B (pulled group) is 1 nm
> (10 Angs) then I intend to run 10 windows after each 1 Angstrom. Due to
> some reasons I want to use restart file of previous window, so if suppose
> 1st window (10 Angstrom window) is done then I will use last restart file
> of 1st window for 2nd window (9 Angstrom window)
>
> (This is different from Justin's tutorial in which initial configurations
> are generated in single pulling experiment).
>
>  In such case as I said I want to use last restart of 1st Window for 2nd
> window so obviously the distance will not be exactly 9 Angstrom between A
> and B for 1st window restart file. What approach I should use for adjusting
> initial distance being 9 Angstrom to get initial configuration for 2nd
> window
>
> Knowing the distance between A and B in the restart file of 1st window
> (say 'x')
> then for second window y = 9 - x (where x can be > or < 9),
>
>
> First approach:
>
> pull_rate1      = (y/1000) or even slower
>
>
> Second approach:
>
> pull_init1      = y
> pull_rate1      = 0.0
>
>
> Please Note for both the cases I can use pull_vec1 or pull rates (- or +)
> for positive or negative relative movement to get exact 9 Angstrom window
> distance
>
> regards,
> Jiomm
>