Hi,
On Thu, Jun 14, 2012 at 11:33 PM, Soumya Lipsa Rath
<soumyalipsabt.gmail.com> wrote:
> I am trying to run Replica exchange MD simulation implicitly. During the
> equilibration step and at higher temperatures, the structure of my protein
> becomes distorted.
>
> During the MD run (in explicit solvent) I did not see any loss of
> secondary structure..
Just to clarify, in your original post you wrote that you saw your
protein begin to unfold (loss of secondary structure etc) using REMD
with implicit solvent. You are comparing this to a previous normal MD
run in explicit solvent at high temperature, where you did not see any
loss of secondary structure.
The problem here is that you are comparing two very different
timescales. You don't say how long you ran either of the simulations,
but in your REMD simulation you are first enhancing sampling with
replica exchange, then further enhancing sampling by using implicit
solvent (you don't say what thermostat you use and whether you employ
an NP term, which will also affect sampling). In contrast, you would
have to run the same system using normal MD with explicit solvent way
way way longer to see the same behavior. Unless you are convinced that
both the REMD and MD simulations are even somewhat converged I don'
think you should directly compare them.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Jun 15 2012 - 06:30:03 PDT
