mohsen ramezanpour wrote:
Dear Dr.Justin
Regarding Umbrella Sampling tutorial:
The CONTINUATION option in md_umbrella.mdp is YES,
and you have noticed : From NPT
I can't understand it's reason correctly!
This is a meaningless comment. It was left there from copying and pasting files
before modifying them. The important part is that "continuation = yes" be set
to correctly solve the constraints.
we run a NPT and then Pulling, then extracted some configurations from
pull.trr file.
I think we must continue from pull.cpt not NPT.cpt
I mean :
grompp -f md_umbrella.mdp ............................. -t pull.cpt
is more correct than
grompp -f md_umbrella.mdp .............................. -t NPT.cpt
am I right?
In the case of the tutorial, no. There is not a corresponding .cpt file for
each configuration generated. If you were to somehow apply the same .cpt file
for each configuration, almost certainly some of the windows would blow up
because the initial velocities would cause nasty collisions. Note that I
discuss the continuation issue, proper settings for gen_vel, etc. in the
tutorial, step six.
-Justin
Thanks in advance for your reply
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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