On 6/7/13 7:41 AM, gromacs query wrote:
Dear All,
Please any suggestion?
I think you should be able to set whatever value you like for pull_init1 and the
code should take care of it.
-Justin
On Mon, Jun 3, 2013 at 4:53 PM, gromacs query <gromacsqu...@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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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