Re: Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers)

From: Brian Radak (
Date: Mon Apr 04 2016 - 09:44:37 CDT

I believe all thermostats are mutually exclusive at present. You might
be able to "turn off" langevin dynamics by specifying non-uniform
friction coefficients with some atoms set to zero, but I have not tried
this. Looking at the code, it looks like this ought to work and can
already be done for hydrogens (see src/Sequencer.C in
langevinVelociitesBBK1(), for example).

The drag/noise terms in Langevin definitely do not have knowledge of
direction at this time - the velocity vectors are just scaled uniformly.
You might be able to modify the integrator for this.


On 04/04/2016 07:16 AM, Loison Claire wrote:
> Dear NAMD-users and developers,
> I simulate all-atom hydrated fluid lipidic bilayers, eventually with
> some flows,
> and I would like to use a thermostat which perturbs not too much the
> flows in the systems.
> I have tried the Lowe-Andersen thermostat and it seems to be
> reasonable for equilibrium diffusion in the water
> (similar diffusion in NVT and NVE ensembles),
> but the lipidic diffusion is perturbed by the thermostat.
> Therefore, I would like to try using the Lowe-Andersen thermostat for
> water atoms only.
> Would it be possible to have,
> as for Langevin or T-coupling thermostats,
> a pdb file where a given column provides
> coupling factors for each atoms individually ?
> Would that be difficult to implement in NAMD ?
> Similarly, is it possible to thermostate in chosen directions only
> (X,Y or Z...) ?
> Typically, with an electric field, I do not want to thermostate in
> that direction, but
> the results remains not too false if one thermostates in the other
> directions
> From the UG, I had the impression that it is not implemented.
> I understand that for Lowe-Andersen this is not possible, but
> maybe this would be already helpfull using Langevin thermostat...
> Naively, it seems to me that a direction-selective thermostat
> should be relatively easy to implement
> (having a zero coupling for selected directions for instance)
> but I have no experience at all with NAMD development,
> would somebody have some hint where to begin with, and
> maybe what not to forget...
> Thank you in advance for any help.
> Best regards,
> Claire Loison

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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