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

Subhrangshu Supakar ssupakar at gmail.com
Tue Oct 26 10:05:32 CEST 2010


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
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