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

From: Loison Claire (cloison_at_lasim.univ-lyon1.fr)
Date: Mon Apr 04 2016 - 07:16:22 CDT

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
 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

Chargée de Recherches CNRS
Theoretical Physical Chemistry Group
    Institut Lumière Matière
    UMR 5306 CNRS/UCBL
    Bat. Alfred Kastler, RdC
    43, bd du 11 Novembre 1918
    Tel      +33 4 72 43 12 57
    Fax      +33 4 72 43 15 07
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