Subhrangshu Supakar wrote:
Hi!!
I am new to short peptide simulations at low temperatures.
I want to run a MD of short peptides of 6 - 12 residues at 276 K.
For this the scheme I wish to follow is :
1. Run a short energy minimization of the peptide + water system to
remove short contacts
2. Equillibrate the system at 2K for 100ps
3. Rum MD with a starting temperature of 2K and finally taking it to
276K in ~ 120ps in 15 annealing points and continue for ~ 50 - 100 ns
Is this OK or do I have to Equilibrate the system at ~298K and in MD
take the temp from 2K to 276 K and continue for 50 ns.
And why would you have to do that? The purpose of equilibration is to relax
your system under the desired conditions.
The other thing to worry about is whether or not your water model is valid at a
point just above freezing.
-Justin
Please help. Thanks in advance
Subhrangshu Supakar
India
--
========================================
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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