Yes one should always use restraints when relaxing initial coordinates. The
tutorial is not meant as an example of a good equilibration protocol. In my
lab we use a protocol that involves many stages. The details depend greatly
on the system being studied and how the coordinates were built. I suggest
reading literature on projects with goals similar to your and adapting their
protocol.
On May 11, 2011 6:24 AM, "Sangita Kachhap" <sangita.imtech.res.in> wrote:
Hello All
I have a confusion about explicit solvent and implicit solvent MD
simulation.
As I have learned till now that during explicit MD simulation in heating
step
apply of small positional restraint on backbone to avoid any wired changes
in
structure
during heating from 0-300K.
I have to do MD simulation using implicit solvent condition.
When I go through AMBER basic tutorial of DNA MD simulation,in explicit
solvent
positional
restraint has applied on DNA but in case of implicit there is no any
positional
restraint on DNA.
My question is in case of explicit solvent when heat up the system there is
requirement of
positional restraint.
So will not be requirement of positional restraint on system when using
implicit
solvent during heating?
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Wed May 11 2011 - 06:30:03 PDT
