Hi all,
The diffusion coefficient can be calculated for the all the waters in the
system, but how do calculate it for just the water molecules which are within
0.5 nm of the protein? Does anyone have any experience with this?
I've tried to use gmx select to write an index file for the waters bu
On 9/17/17 6:05 PM, Dallas Warren wrote:
http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html
Don't know exactly how to do it myself, but there will be an option
there where you can specify the z coordinate as a way to break it up
into groups.
And herein lies the challenge.
http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html
Don't know exactly how to do it myself, but there will be an option
there where you can specify the z coordinate as a way to break it up
into groups.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash I
Any help!
On Saturday, September 16, 2017, Sohaib. Mohammed <
sohaibmohamme...@gmail.com> wrote:
> Hey Users,
>
> I want to calculate the diffusion coefficient using gmx msd. I want to
> divide the box into slices of 5 A parallel to z axis and calculate the
> diffusion coefficient for each slice.
Hey Users,
I want to calculate the diffusion coefficient using gmx msd. I want to
divide the box into slices of 5 A parallel to z axis and calculate the
diffusion coefficient for each slice. My question is how to make these
slices, I've tried gmx trajconv but didn't work with me. I believe it's
qu
Hey Users,
I want to calculate the diffusion coefficient using gmx msd. I want to
divide the box into slices of 5 A parallel to z axis and calculate the
diffusion coefficient for each slice. My question is how to make these
slices, I've tried gmx trajconv but didn't work with me. I believe it's
qu
The following paper may also be interesting.
"System-size corrections for self-diffusion coefficients calculated from
molecular dynamics simulations: The case of CO2, n-alkanes, and
poly(ethylene glycol) dimethyl ether" J. Chem. Phys. 145, 074109 (2016);
http://dx.doi.org/10.1063/1.4960776
2016-
See the following paper
(http://pubs.acs.org/doi/abs/10.1021/ct400109a) for some examples of
diffusion calculations in GROMACS.
The finite size correction for diffusion coefficients is something
different than the long range energy corrections. A discussion of this
(I can't vouch for all the detai
Hi,
I would also consider using a pressure-coupling algorithm that isn't known
to create the wrong velocity distribution.
Mark
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www
te: Wed, 17 Aug 2016 13:11:02 -0400
From: Justin Lemkul
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Diffusion coefficient water
Message-ID: <8eb7b1ee-041c-906d-f7a1-7e6d683c4...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 8/17/16 11:28 AM, Diez Fernandez,
sage: 1
>Date: Wed, 17 Aug 2016 21:49:45 +0530
>From: Nikhil Maroli
>To: gromacs.org_gmx-users@maillist.sys.kth.se
>Subject: Re: [gmx-users] Diffusion coefficient water
>Message-ID:
>
>Content-Type: text/plain; charset=UTF-8
>
>I don't think we can reproduce t
4. you could even try NVT ensemble
2016-08-18 2:25 GMT+08:00 li he :
> I think you could try following things to see if you could get 'better'
> results
> 1. use time step of 0.2 or even 0.1 fs
> 2. try different tau-t and tau-p, e.g. use larger tau-t
> 3. try different p-coupling methods
>
> 201
I think you could try following things to see if you could get 'better'
results
1. use time step of 0.2 or even 0.1 fs
2. try different tau-t and tau-p, e.g. use larger tau-t
3. try different p-coupling methods
2016-08-17 23:28 GMT+08:00 Diez Fernandez, Amanda <
amanda.die...@imperial.ac.uk>:
> D
On 8/17/16 11:28 AM, Diez Fernandez, Amanda wrote:
Dear Gromacs users,
I was trying to reproduce the published values for the diffusion coefficient of
SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in some of my
simulations and I am failing to do so.
More worryingly I get differen
I don't think we can reproduce the exact results in MD .The overall
behaviour of the system will be same .so it's obvious
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.groma
Dear Gromacs users,
I was trying to reproduce the published values for the diffusion coefficient of
SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in some of my
simulations and I am failing to do so.
More worryingly I get different results for different identical runs.
I am using a 2n
On 7/23/14, 7:13 AM, Meena Singh wrote:
Dear GROMACS users,
I'm working on the diffusivity of metal ion with its ligand in organic
phase.
I want to calculate the diffusion coefficient of metal-ligand complex as a
group, but when I run g_msd command the option are there for only
individual mol
Dear GROMACS users,
I'm working on the diffusivity of metal ion with its ligand in organic
phase.
I want to calculate the diffusion coefficient of metal-ligand complex as a
group, but when I run g_msd command the option are there for only
individual molecules diffusivity calculation.
Can I calcu
18 matches
Mail list logo
