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

[Subhrangshu Supakar]

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.

Please help. Thanks in advance


Subhrangshu Supakar
India
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101026/ae48e7e4/attachment.html>