Re: all atom simulations with explicit water molecules and langevin thermostat

From: Margaret S. Cheung (
Date: Fri Oct 05 2007 - 09:54:20 CDT

Dear Balazs,
Thank you for the links and references. The "double-counting" of
frictions derived from solvents confused me and now I think if I am only
interested in the thermodynamics property of a peptide, a low friction
value should be OK.


Jojart Balazs wrote:
> Dear Margaret,
> this question was discussed in the amber community also, check the
> following mails:
> Hope this helps,
> Balazs
> Margaret S. Cheung írta:
>> Hi,
>> I thought that langevin dynamics is to approximate solvent dynamics
>> implicitly. In the NAMD script setting of all-atomistic simulations,
>> the langevin thermostat is turned on even explicit water molecules
>> are included. Could someone please shed light on me as I was confused
>> by this configuration? We ran all-atom simulations with and without
>> langevin thermostat and the energy distribution from both looked
>> different. Did user normally include langevin thermostat for all-atom
>> simulations with explicit water molecules? I google this question but
>> without much success in return. If someone has links to refer answers
>> to this question, please kindly let me know, too.
>> Thank you.
>> Sincerely,
>> Margaret Cheung

Margaret S. Cheung
Assistant Professor
Department of Physics
629C Science and Research 1
University of Houston
Houston, TX 77204-5005
(O)713-743-8358 (F)713-743-3589

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