[gmx-users] Langevin dynamics

[syma]

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,

-Syma

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Berk Hess
Sent: 04 July 2006 13:50
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Langevin dynamics




>From: "syma" <syma.khalid at bioch.ox.ac.uk>
>Reply-To: syma.khalid at bioch.ox.ac.uk,Discussion list for GROMACS users 
><gmx-users at gromacs.org>
>To: "'Discussion list for GROMACS users'" <gmx-users at gromacs.org>
>Subject: [gmx-users] Langevin dynamics
>Date: Tue, 4 Jul 2006 11:06:35 +0100
>
>Hi,
>
>I am still trying to do Langevin dynamics in gromacs- does anyone know 
>(ball
>park) what would be reasonable values to use for the frictional term when
>simulating helical peptides in solution?

You did not give enough information.

Are you using explicit or implicit solvent?

With implicit solvent you can use Stokes law to estimate the value.
But Gromacs does not come with an implicit solvent force field.
Any explicit solvent force field will give completely wrong results
if you just leave out the solvent.

Berk.


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