[gmx-users] Re: using previous window restart file
jalemkul at vt.edu
Fri Jun 7 13:46:04 CEST 2013
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.
> 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
>> 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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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