bipin singh wrote:
Thanks for your comments
I have a very crude question which may not be even logical to ask here
but I just want to know your opinion on this:
If I will perform two simulations in following two ways :
*RUN:1*
(1) Did NVT with POSRES on protein and
gen_vel=yes
gen_temp= 350
(2) Did NPT with POSRES on protein and
continuation=yes
gen_vel=no ;Without reading velocities from NVT
(3) Did MD with No POSRES (NPT)
continuation=yes
gen_vel=no ; No velocities read from previous run
*
RUN:2
*(1) Did NVT with POSRES on protein and
gen_vel=yes
gen_temp= 350
(2) Did NPT with POSRES on protein and
continuation=yes
gen_vel=no ; Reading velocities from NVT run using -t option
(3) Did MD with No POSRES (NPT)
continuation=yes
gen_vel=no ; Velocities read from previous run using -t option
What will be the expected flaws of the RUN:1 over RUN:2 and will the
results got from the RUN:1 is unreliable ? If yes why ?
I doubt there is a sound way to predict the errors that will arise. In the case
of method #1, you obliterate any benefit of prior equilibration. At the outset
of your unrestrained MD, your equilibrated ensemble is no more. Thus, your
system will essentially start at some undefined ensemble and require a long time
to re-establish equilibrium. There may be algorithmic problems with thermostats
and barostats as they try to establish the target values, which will depend on
exactly which algorithms you're using.
-Justin
--
========================================
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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