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Re: why I cannot read coordinate and veloci files by traj or merge?
dswei #31324 01/24/13 07:02 PM
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Is there a specific reason to use langevin dynamics?

Re: why I cannot read coordinate and veloci files by traj or merge?
dswei #31326 01/24/13 09:09 PM
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It should be noted that using Langevin dynamics does affect the timescale of simulation events; rates, diffusion, and other properties cannot easily be compared to experiments. If you just want T control, there are better options available in CHARMM than using Langevin.


Rick Venable
computational chemist

Re: why I cannot read coordinate and veloci files by traj or merge?
dswei #31327 01/24/13 09:58 PM
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Yeah that's what I was aiming at.

Re: why I cannot read coordinate and veloci files by traj or merge?
dswei #31328 01/25/13 10:13 AM
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I don't use PBC (notice nbfrq set to zero) and I fit the experimental diffusion to lambdas/Qs friction. In a more (very) personal note, I only trust the equations that I understand from white noise stat mech (lambda in LANG and Q in NOSE-H) and others CPT/vel scaling, etc seem for the time being too phenomenological for me (compressibility, etc). But as all in life I am looking forward to being terribly wrong. Interesting, should I open a new topic for this?

Re: why I cannot read coordinate and veloci files by traj or merge?
dswei #31330 01/25/13 02:06 PM
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INBFRQ 0 disables all non-bond updates, and would be expected to have very bad consequences in most cases. It has nothing to do with PBC.

Unless you choose to use the wretched Berendsen weak coupling, the CPT code is based on the extended system approach from the work of Nose, Hoover, and HC Andersen; see the citations in pressure.doc


Rick Venable
computational chemist

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