Hello,
I have a comment regarding the Gromacs manual. For equation (3.62) in
Chapter 3.8, \epsilon_i is called the friction constant. This is incorrect
since in that equation \epsilon is actually collision frequency and should
be represented with the letter \gamma. The product of the collision
fre
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
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
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 c
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
Hi:
Thanks to everybody who helped me out with my last email. But now I
have another problem and I hope you can help me. As i told you I'm
doing a simulation of polyelectrolyte chain consisting of 50 charged
beads (-1) with 50 charged counterions(+1). My box
simulation is 400 nm x 400 nm x 400 nm
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:
Hi,
I have been having a few problems running Langevin dynamics and was
wondering if anyone can help.
I have run both atomistic and coarse grain LD simulations in gromacs 3.1 3.2
and 3.3. The puzzling thing is that changing the value of the frictional
constant makes no difference to the simulatio
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 d
Hi,
I am still trying to do Langevin dynamics in gromacs- does anyone know (ball
park) what would be reasonable values to use for the frictional term when
simulating helical peptides in solution?
Many thanks in advance,
-Syma
***
Dr Syma Khalid
Hi,
I would appreciate some advice on running Langevin dynamics in GROMACS. I
plan to do a coarse-grained simulation in vacuo (ie 4 'atoms' to 1 particle)
and was wondering what sort of value to use for the frictional term? I'm
guessing that as each particle is heavier than in atomistic simulation
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