Dear Sir,
I went through the model.top script and and tried to understand that how it
works. But there are few problems in understanding that script, please guide
me for these mentioned problems.
1. In OPTIMIZE process (VTFM optimization), the addition of restraints is
governed by PICK_RESTRAINTS which in turn depend on SCHEDULE file (3rd
column, NRNG), meaning thereby that only those restraints will be taken into
consideration which applies on atoms, which comes in category as specified
by Schedule file (3rd column). Although in .log file I found restraints are
added step by step (N_SCHEDULE step) during optimization , are the atoms
also added continously, or just explain a bit how this profile goes?
2. Out of curiosity I ask this question, if all restraints and all atoms are
taken into consideration at a time, and then optimization is done, will that
be better/efficient than the method it takes in model.top?
3. Also, I observed that this addition of restraints (for every N_SCHEDULE
step) during optimization increases the value of objective function , and it
finally stops at a higher value, will that value be considered final one or
various such consequent optimization cycles should be carried out to finally
lower down the value?
Please reply , I will be very thankful to you.
Hope to receive explainatory reply.
Thanking you in advance,
sincerely,
--
VIVEK SHARMA
Graduate Student,
(Biochemistry/Biophysics)
University of Helsinki