Dear dac,
Thanks a lot for your reply and apologies for being that approximative
in the explanation of my issue.
By the way you gave me the solution though, as the problem was that I was
plotting VOLUME and DENSITY from the NVT run, using the script
"process_mdout.perl" taken from one of your tutorials.
Actually the script took some values from the output file which had nothing
to do with volume and density.
With regard to the taup value, I had noticed that the ones used in the
tutorials are larger, but as long as I have a "good" equilibration
the simulation is fine, isn't it?
Many thanks and best wishes,
MP
2011/5/14 case <case.biomaps.rutgers.edu>:
> 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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--
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 Sat May 14 2011 - 09:00:02 PDT
