From: "Syma Khalid" <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
To: "'Discussion list for GROMACS users'"
Subject: [gmx-users] langevin dynamics
Date: Tue, 30 Oct 2007 16:55:59 -
Dear all,
I was wondering if someone could offer some advice?
I
Syma Khalid wrote:
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?
If you take a point charge and a blob with opposite charge and do some
va
Just my unasked-for two cents: Langevin dynamics in water is probably
a poor substitute for some representation of water. Langevin can
provide some of the friction/noise of water -- but electrostatics
interactions are very different in water than in vacuum. Langevin
dynamics is probably not a subst
/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
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 simu
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
If you want to use BD, the friction coefficient has to be large. Please
check the manual. If you change your bd-fric to 5000, it might help.
On Wed, 2006-08-02 at 23:24 +0800, PAUL NEWMAN wrote:
> Hi:
> Thanks to everybody who helped me out with my last email. But now I
> have another problem a
07:21:46 -0700
From: "David Mobley" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] langevin dynamics
Gerrit is right, with "sd", the friction is set by tau_t, as described
in the section on SD in the manual. In my hands, different tau_t with
sd does make a significant diff
On 7/31/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:Send gmx-users mailing list submissions toDate: Mon, 31 Jul 2006 07:21:46 -0700
From: "David Mobley" <[EMAIL PROTECTED]>Subject: Re: [gmx-users] langevin dynamicsGerrit is right, with "sd", the friction is set by tau_t, as described
in the se
Gerrit is right, with "sd", the friction is set by tau_t, as described
in the section on SD in the manual. In my hands, different tau_t with
sd does make a significant difference in what goes on...
David
On 7/31/06, Gerrit Groenhof (RUG) <[EMAIL PROTECTED]> wrote:
I think you do not use the bd
I think you do not use the bd_fric in combination with sd, but with bd,
the friction is set by the tau_t instead. Did you als use different
parameters for that?
For bd, you would use the friction bd_fric to set the ld friction, but
not for sd, but I could be wrong here...
Gerrit
syma wrote:
From: "syma" <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
To: "'Discussion list for GROMACS users'"
Subject: RE: [gmx-users] Langevin dynamics
Date: Tue, 4 Jul 2006 13:59:06 +0100
Hi,
Thanks.
Ok so some more inf
s to drift. I thought using Langevin dynamics might prevent this.
Any ideas would gratefully received,
-Syma
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Berk Hess
Sent: 04 July 2006 13:50
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Langevi
From: "syma" <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
To: "'Discussion list for GROMACS users'"
Subject: [gmx-users] Langevin dynamics
Date: Tue, 4 Jul 2006 11:06:35 +0100
Hi,
I am still trying to do Langevin dynamics in gromacs- does anyone know
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