From: "syma" <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
<[email protected]>
To: "'Discussion list for GROMACS users'" <[email protected]>
Subject: RE: [gmx-users] Langevin dynamics
Date: Tue, 4 Jul 2006 13:59:06 +0100
Hi,
Thanks.
Ok so some more info:
I am developing a coarse-grained model of peptides based on an elastic
network approach. Rather than run the simulations in vacuum I wanted to use
Langevin dynamics to dampen the motions.
Also, at the moment if I simulate very long, thin polymers I get big
fluctuations in my energies (have tried NVT, NPT and NVE). I have tried to
reduce the time step, but this does not solve the energy problem.
So the simulation starts off ok- the energy is fine- but after a time, the
ends of my polymer start to 'waggle' a lot and this is when the energy
begins to drift. I thought using Langevin dynamics might prevent this.
Any ideas would gratefully received,
Read some literature on polymers.
Polymer dynamics can be nicely decribed by normal modes.
Starting from a "perfect" straight conformation will cause
the modes to start syncronized and you should indeed see large
energy fluctuations.
Berk.
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