On 12/10/11 3:23 AM, Matthew Zwier wrote:
Hi Ruhollah,
A while ago on the list there was a discussion of extreme memory use
and possibly-incorrect results from g_msd under some conditions. The
problem could be worked around by imaging the trajectory with trjconv
first to remove jumps across the
Hi Ruhollah,
A while ago on the list there was a discussion of extreme memory use
and possibly-incorrect results from g_msd under some conditions. The
problem could be worked around by imaging the trajectory with trjconv
first to remove jumps across the box, then running g_msd on the
results. Pe
David,
thank you for your reply.
but, g_msd gives a diffusion coefficient which is one order of magnitude
higher than expected for a small polypeptide (15 res long with gyration Rg
~ 0.8nm) with the same size. this is command line i used:
g_msd-mpi -f md_mine_2nd.xtc -s md_mine_2nd.tpr -o msd_2
On 2011-12-09 08:34, Mark Abraham wrote:
On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote:
I want to calculate the diffusion coefficient of a small polypeptide
with g_msd (see here
http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant)
because of periodic boundary condition, when t
On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote:
I want to calculate the diffusion coefficient of a small polypeptide
with g_msd (see here
http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant)
because of periodic boundary condition, when the peptide goes out of
the right side i
I want to calculate the diffusion coefficient of a small polypeptide with
g_msd (see here
http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant)
because of periodic boundary condition, when the peptide goes out of the
right side it comes in from left side, which leads to an artificial
di
Chih-Ying Lin wrote:
Hi
I calculated the diffusion coefficient for lysozyme and get ~4x1e-6 (cm2/s)
But, the experimental data is around 1x1e-6 (cm2/s).
How could I explain for this discrepency?
If the simulation is based off of a simulation of a single lysozyme protein in
water, I'd be a
Hi
I calculated the diffusion coefficient for lysozyme and get ~4x1e-6 (cm2/s)
But, the experimental data is around 1x1e-6 (cm2/s).
How could I explain for this discrepency?
Thank you
Lin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please
diffusion coefficient and it
combines well with the Gromos force fields, so use that.
It is well known that the diffusion of SPC is twice what it should be.
Berk
> Date: Wed, 10 Mar 2010 07:35:41 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-user
Sunil Thapa wrote:
Respected Experts
I need your help
In my study of diffusion of a oxygen molecule in 255 molecules of water,
I previously used SPC water model with ffgmx force field with cutoff L-J
and Coulomb interaction. I wanted to reproduce the experimental value
2.4 unit for diffusi
Respected Experts
I need your help
In my study of diffusion of a oxygen molecule in 255 molecules of water, I
previously used SPC water model with ffgmx force field with cutoff L-J and
Coulomb interaction. I wanted to reproduce the experimental value 2.4 unit for
diffusion coefficient of oxyge
Hi,
If i remember correctly SPC/E water might be worth trying. There is plenty
of research paper in this field. Try this paper
http://pubs.acs.org/doi/abs/10.1021/jp003020w
Also P,T coupling have effects on Diffusion Coeff.
amit
On Fri, Mar 5, 2010 at 1:29 AM, Sunil Thapa wrote:
> Respected
Sunil Thapa skrev:
Respected experts
I want to calculate the self diffusion cofficient of an oxygen
molecule in water. The experimental value in the literature is found
to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have
considered cut-off Lennard Jones interaction between wat
Respected experts
I want to calculate the self diffusion cofficient of an oxygen molecule in
water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s
at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones
interaction between water and oxygen. I want
10 ps is too short of a trajectory, even for such a large system (for pure
water it is considered large). i would guess that it is a typing-error and
you ran for 10 ns?
omer.
On Wed, Feb 10, 2010 at 11:05, Amit Choubey wrote:
> I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I
>
Hi,
you already have your solution at hand.
On 10.02.2010, at 10:05, Amit Choubey wrote:
> Hi Everyone,
>
> I have been trying to calculate diffusion coefficient for water. I am trying
> to reproduce the numbers published in journal papers.
> I am using SPCE water model. I use the g_msd analy
Hi Everyone,
I have been trying to calculate diffusion coefficient for water. I am trying
to reproduce the numbers published in journal papers.
I am using SPCE water model. I use the g_msd analysis tool.
g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8
I use a box of volume 6x6x6 nm^3 which h
Erik Marklund wrote:
Hi users,
I have simulated a box of NVT-water, more specifically the flexible
urey-bradley-like TIPS-reparametrisation by Dang and Pettitt (1987).
What I notice is that the diffusion coefficient increases when I
calculate it from a longer snippet from my trajectory. If I
Hi users,
I have simulated a box of NVT-water, more specifically the flexible
urey-bradley-like TIPS-reparametrisation by Dang and Pettitt (1987).
What I notice is that the diffusion coefficient increases when I
calculate it from a longer snippet from my trajectory. If I use only 100
ps; star
Sarah Witzke wrote:
Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole
Sendt: fr 05-06-2009 13:32
Til: Discussion list for GROMACS users
Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd
Sarah Witzke wrote:
Dear XAvier,
Thank you very much for your answer. I have
Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole
Sendt: fr 05-06-2009 13:32
Til: Discussion list for GROMACS users
Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd
Sarah Witzke wrote:
> Dear XAvier,
>
>
>
> Thank you very much for your answer. I have post
Emne: Re: [gmx-users] diffusion coefficient with g_msd
On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote:
Dear gromacs users,
I have done several simulations with small lipophilic, molecules
diffusing into a DMPC bilayer.
I would like to calculate the diffusion coefficient of the molecu
r 05-06-2009 09:34
Til: Discussion list for GROMACS users
Emne: Re: [gmx-users] diffusion coefficient with g_msd
On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote:
> Dear gromacs users,
>
>
>
> I have done several simulations with small lipophilic, molecules
> diffusing into a
On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote:
Dear gromacs users,
I have done several simulations with small lipophilic, molecules
diffusing into a DMPC bilayer.
I would like to calculate the diffusion coefficient of the molecules
inside the membrane, and therefore I looked at g_msd.
Dear gromacs users,
I have done several simulations with small lipophilic, molecules diffusing into
a DMPC bilayer.
I would like to calculate the diffusion coefficient of the molecules inside the
membrane, and therefore I looked at g_msd. The manual (version 4.0) states on
p. 250 (manual pa
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