From: Margaret S. Cheung (mscheung_at_uh.edu)
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.
Sincerely,
Margaret
Jojart Balazs wrote:
> Dear Margaret,
>
> this question was discussed in the amber community also, check the
> following mails:
> http://amber.ch.ic.ac.uk/archive/200708/0456.html
> http://amber.ch.ic.ac.uk/archive/200708/0460.html
> http://amber.ch.ic.ac.uk/archive/200708/0461.html
>
> 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 email: mscheung_at_uh.edu (O)713-743-8358 (F)713-743-3589 http://www.phys.uh.edu/~mscheung/
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