[gmx-users] Brownian dynamics

Yin Jian smayinj at nus.edu.sg
Wed Dec 26 10:26:52 CET 2007


Hi Mark,
Thanks for your time.
The page you directed me to go tell me the following information:
--------------------------------------
Note that Langevin dynamics is not a magic option that allows the
solvent to be replaced by a vacuum. Since it adds friction and noise it
only influences the dynamics, not distributions. A high friction value
may mimick the friction of water, however it does nothing to the
potentials. Using Langevin dynamics without water is just a vacuum
simulation.
---------------------------------------
1) what is the definition of the "potential" in it?
2) never heard langevin dynamics used water, can you give me a
literature
   using water in langevin dynamics simulation?
3) why it says the friction in langevin dynamics does nothing to the  
   "potential"?

Sorry for my stupid questions. Anyway I just want to learn more.


Thanks and happy new year


Regards,
Yin Jian 

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Monday, December 24, 2007 6:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Brownian dynamics

Yin Jian wrote:
> Hi Berk,
> I am looking for a way to be able to run MD faster without
> Explicit solvent component. Brownian dynamics (I mean langevin
> Dynamics) is way out I think. But I am not sure the package
> Implemented in Gromacs is a good one or not yet. Since I have
> Seen no one using it in the literature yet, right?

http://wiki.gromacs.org/index.php/Langevin_Dynamics

Mark
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



More information about the gromacs.org_gmx-users mailing list