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

From: Jojart Balazs (jojartb_at_pharm.u-szeged.hu)
Date: Fri Oct 05 2007 - 05:41:14 CDT

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
>

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