Re: (is there) a dependence of dynamics on WRAPPING

From: Giacomo Fiorin (
Date: Sat Aug 15 2009 - 08:59:46 CDT

Hi Satya, all MD trajectories with a common starting point diverge
very soon, due to different random numbers in the Langevin, or simply
a different order of the operations in the CPUs. Wrapping may affect
this, as well. Both trajectories, though, have an equal chance to
explore the equilibrium ensemble of the protein.


---- ----
 Giacomo Fiorin
   ICMS - Institute for Computational Molecular Science
     Temple University
     1900 N 12 th Street, Philadelphia, PA 19122
 work phone: (+1)-215-204-4216
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 mail: giacomo.fiorin_<at>
---- ----

On Sat, Aug 15, 2009 at 2:33 AM, satya work<> wrote:
> Dear all,
> I have a concern about wrapping in NAMD.
> I have equilibrated a small protein-bilayer system for about 15 ns. After
> this I ran two sets of simulations with exactlly the same initial conditions
> except in one case WRAP was off and in the other WRAP on. I look at the RMSD
> of protein to check that it has equilibrated etc.,
> I ran 5ns in each case and was interested in calculating protein-lipid
> contacts and I get quite different answers. May be this is because of the
> Langevin piston (introducing random ness) used in the simulation, but still
> I am concerned about this.. It is possible that my system has not
> equilibrated yet, and this could be a problem of sampling.
> Any suggestions?
> Satya

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