On Fri, May 13, 2011, Massimiliano Porrini wrote:
>
> 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).
There is no enough information given to help much, but it sounds like you
may have used the wrong restart file(?) when beginning the "production" run.
Have you looked carefully at the "production" output (by hand)? Your values
for volume and density go to zero, which is odd. Note that the volume and
density are not printed out in an NVT run; is it possible that your graphing
script is looking for something that is not there, and plotting zero?
>
> 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)
Aside: this is really way too short a value for taup; consider values at least
an order of magnitude bigger.
....dac
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Received on Sat May 14 2011 - 07:00:02 PDT
