Dear all,
I am equilibrating my 16k atoms system (a peptide in a truncated
octahedron box of water) and I see
a "huge suspicious" contraction of the volume upon the beginning of
the production run (NVT Langevin dynamics).
Even the density behaves weirdly and
I attached a graph to show this behaviour (the production run starts at 500 ps).
Besides, during the equilibration process energies, density and volume
etc. look fine!
I used the following protocol (after minimization) to equilibrate the system:
- Langevin NVT at 300 K for 100ps (gamma_ln = 5.0)
- NPT at 300K and 1 atm for 400ps (gamma_ln = 5.0 and taup = 0.1)
and then for the production run I am using the following parameters:
- Langevin NVT at 300K (gamma_ln = 3.0).
Any idea/hint about this behaviour would be really appreciated.
Regards,
MP
--
Dr Massimiliano Porrini
P. E. Barran Research Group
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Fri May 13 2011 - 06:00:03 PDT
