[gmx-users] Help for MD of short peptides at 276K

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 26 13:05:49 CEST 2010

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.


> Please help. Thanks in advance
> Subhrangshu Supakar
> India


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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