[gmx-users] using previous window restart file

gromacs query gromacsquery at gmail.com
Mon Jun 3 15:53:41 CEST 2013

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

Knowing the distance between A and B in the restart file of 1st window (say
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


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