[gmx-users] langevin dynamics

[Georgios Patargias]

Hi Syma

I think that Gromacs applies a neutralising charge distribution if there is 
a charged system. 

Best wishes 
George

Dr. George Patargias
Polymer IRC Group
University of Leeds
Leeds, LS2 9JT, UK



-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Syma Khalid
Sent: Tue 10/30/2007 5:30 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] langevin dynamics
 
Hi Mark,

Firstly, thanks for your prompt response.
If they really are just counter-ions, then simple electrostatics will do 
that... this is a side-issue, however.

Please can you explain the above? Will the ions simply collapse onto my
protein?

The counter ions are simply to there to give me an overall neutral system.
Is there some other way I can get a neutral system?

Many thanks,

-Syma

***********************************************************************
Dr Syma Khalid 
RCUK Fellow (Chemical Biology)              
School of Chemistry
University of Southampton	
Highfield			 	
Southampton      phone: (0)2380-594176
SO17 1BJ          email: S.Khalid at soton.ac.uk    			
U.K.
***********************************************************************
 

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Mark Abraham
Sent: 30 October 2007 17:25
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] langevin dynamics

Syma Khalid wrote:
> Dear all,
> 
>  
> 
> I was wondering if someone could offer some advice?
> 
> I would like to run an atomistic langevin dynamics simulation (as I 
> don't want to include water explicitly). If I add the appropriate 
> langevin dynamics options in the mdp file, then is there any reason why 
> I shouldn't use explicit counter ions (unfortunately my protein has an 
> overall charge)?

In what medium are they going to move? How realistic is that going to be?

> Obviously I would use periodic boundary conditions so the ions don't 
> wander off.

If they really are just counter-ions, then simple electrostatics will do 
that... this is a side-issue, however.

Mark
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