[gmx-users] Brownian dynamics

Yin Jian smayinj at nus.edu.sg
Thu Dec 27 04:35:54 CET 2007

Hi Mark,
Thank for your suggestions.
I do not understand why you seems so impatient? But I do remember there
is an old saying:
"there is no stupid question in the world, but there are stupid answers

Now I am confused how to commute with you? Is there somebody Else who
understand me a little better?

Yin Jian

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Wednesday, December 26, 2007 8:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Brownian dynamics

Yin Jian wrote:
> 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
> 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?

The same as in MD? Check out some reference material.

> 2) never heard langevin dynamics used water, can you give me a
> literature
>    using water in langevin dynamics simulation?

Nobody is suggesting this is a good idea.

> 3) why it says the friction in langevin dynamics does nothing to the  
>    "potential"?

Check out the reference material.

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

Teaching you things isn't really our job. You'll get a better response 
from useful people if you've tried to teach yourself and can ask 
focussed questions.

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