Hi,
It seems that the one directional diffusion constants can be obtained by
means of g_msd ...blabla...-type z.
However, my question is that I don't want to obtain the diffusion constants.
Actually, the MSD trajectory file for all 3 dimensional data can be
obtained by conventional g_msd...
I gratefully appreciate to your reply Justin.
You are right, it seems that g_msd provides the MSD.xvg file what I want
(in one direction).
I was confused before.
Thanks again.
2012/11/23 Justin Lemkul jalem...@vt.edu
On 11/22/12 5:44 AM, Kiwoong Kim wrote:
Hi,
It seems that the one
Hi,
I'm not good at shell programming now.
For the simplicity, I wrote down all the gromacs commands in one shell
script.
It means that if I execute the .sh file, then every works including graphs
used for analysis are done.
However, when there are g_msd -f *.xtc -s *.tpr -o *.xvg -rmcomm, I
number in this file. In
your shell script after command line write input.g_rms. when the
command is
executed in shell the file input.g_rms having group number will be read.
Hope it works.
Shahid nayeem
On Fri, Feb 10, 2012 at 4:19 PM, Kiwoong Kim ilmare...@gmail.com
wrote:
Hi,
I'm
Hi,
I have a simulation result from 0 to 50ns after equilibration run.
I want to divide this data set equally into 10blocks (10ns each) and get
block averaged MSD curve (average of 10 blocks).
It seems that I mange to get block MSD data by using g_msd -beginfit 0
-endfit 10, g_msd -beginfit 10
Dear gromacs user
Sorry, my previous question is absolutely wrong. I have simulated MD with
wrong zeolite structure so far.
My question is now turned to find out the correct structure again...
I obtained crystallographic data containing unit cell parameters and space
group, several atom
Hi,
I'm studying the diffusion system of some guest into zeolite structure
(SiO2) assumed to be rigid body.
My question is about making the host neutral.
I obtained the unit cell of zeolite structure from the web.
The structure exhibit net charge. (If I give some charge to Si and O which
Grompy looks like fancy.
Is it reliable for conducting GCMC??
I also need to perform GCMC along with MD.
In Grompy, it seems that the Grompy is compatible with gromacs 4.0.5.
The version of gromacs I use is 4.5.X.
Is it possible to use Grompy with my Gromacs??
2012/1/25 Gianluca Interlandi
0.1098
[ virtualsites2]
; aiajak funct c0 c1
3 1 2 1 -0.5
4 1 2 10.5
[ exclusions ]
3 4
4 3
Below is the previous post message
On 20/01/2012 5:51 PM, Kiwoong Kim wrote:
Hi,
I asked this question
, Kiwoong Kim wrote:
Hi,
Please do keep the discussion on the list, so others can learn and
contribute now and from the archives.
I don’t know how to model N2 molecule yet.
If I use virtual site for N2 model, then, this can be done like below.
Hence, where do I have to apply plus
On 21/01/2012 12:40 AM, Kiwoong Kim wrote:
Hi, Mark.
I'am very grateful to your reply.
I'm sorry not to keep the archive. Actually, I didn't know how to directly
append the reply to the original post because I posted the
previous question under the disabled-subscribed status. I haven't found
Hi,
I asked this question before.
Thanks to Justin, he did reply as follows.
Kiwoong Kim wrote:
Hi,
I'm getting better to use Gromacs owing to many posts on this sites :) .
I have several questions about adding the counter-ions.
My system has a number of N2 molecules which has charge
Hi,
I'm getting better to use Gromacs owing to many posts on this sites :) .
I have several questions about adding the counter-ions.
My system has a number of N2 molecules which has charge, -0.40484(for
single N) X 2.
Thus, I have to add some counter-ions to make the system neutral.
However,
Hi,
I'm trying to plot the displacements in z-coordinate of each particle
belonging to some index group using g_traj.
I typed below thing in prompt
g_traj -f md_0_2_nvt.xtc -s md_0_2_nvt.tpr -n index_traj.ndx -nox -noy -b 0
-e 50 -ox traj -w -xvg xmgrace
There are 6 atoms in the desired index
Hi,
I'm not good at handling Gromacs yet.
My question is about virtual interaction.
I'm doing simulation dealing with CO2 which is linear rigid molecule as you
already know.
As pervasively known, I introduced virtual sites.
However, I don't know how to give initial coordinate correctly of
Hi
I have been learning how to use gromacs owing to your advice.
I have simple question on g_msd.
I tried to plot MSD curve using g_msd. I want to deeply investigate the MSD
curve from 0.01ps to the last of simulation (my case, 1ns).
However, g_msd always produce the MSD curve starting from
Hi,
I need to model linear rigid molecules, CO2.
I understood that the virtual site have to be introduced to model CO2
like below way.
[ atomtypes ]
; type masschargeptype c6c12
D1 22.0049750. A 0. 0.
D2
Hi.
I have questions about calculating the position change of each particles.
Consider there are 4 atoms diffuses into some channel.
Hence, the aim is to calculate position change (only z-axial direction) of
each particles (4 atoms) with respect to time.
I want to keep track of the
Dear members of gromacs
I have several questions.
I have been working on the diffusion problem (diffusing particles diffuse
into the zeolite).
Although I have successfully obtained the output file, there are problems
for analyzing it.
My questions are
1) I have to calculate diffusion
for atom
please let me know how to do it
Thx.
Kiwoong, Kim.
No. 409/Ricci Hall/Dept. of Chemical Biomolecular Engineering/
Sogang University/Sinsoo-Dong/Mapo-Gu/Seoul 121-742/ Korea
(office) +82-2-705-8477
(CP) +82-10-8714-2208
(fax) +82-2-3272-0319
(E-mail) ki...@sogang.ac.kr
on the implicit wall must not be updated.
Hence, I don't know how I can do this kind of thing.
Is there any function to handle the implicit wall that must be rigid and not to
be updated ?
Thx.
Kiwoong, Kim.
No. 409/Ricci Hall/Dept. of Chemical Biomolecular Engineering/
Sogang University
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