From: wzhuang (wzhuang_at_uci.edu)
Date: Thu Oct 04 2007 - 20:16:04 CDT
Hi,Margaret:
My two cents, correct me if I am wrong.
1) 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.
I think when you are using langevin dynamics, you are putting your "system" in touch with a large "bath". your "system" could be only the peptide or the peptide+waterbox. It is used for ensembles such as NPT.
2) We ran all-atom simulations with and without
langevin thermostat and the energy distribution from both looked
different.
I believe, when the system is large enough, in principle, with and without the bath should give you the same thing ( for example, for large system, NVE and NPT give you the same thermo properties ), you got different result might be because your system is practically too small to ignore the pressure fluctuation.
3)Did user normally include langevin thermostat for all-atom simulations with explicit water molecules?
It depends on which ensemble are you using.
2007-10-04
wzhuang
发件人: Margaret S. Cheung
发送时间: 2007-10-04 15:54:49
收件人: namd Entry
抄送: dirar_at_hotmail.com
主题: namd-l: all atom simulations with explicit water molecules and langevinthermostat
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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