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 z-directional
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 1ps.
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'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 dummy
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 g
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, be
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 c
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
usions ]
> 4 3 5
> 5 3 4
> 3 5 4
Thanks Mark again. :)
Have a great day.
2012/1/20 Mark Abraham
> On 21/01/2012 12:04 AM, Kiwoong Kim wrote:
>
>
>
> Hi,
>
>
> Please do keep the discussion on the list, so others can learn and
> contribute now and from the arc
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
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
>
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
satisf
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 coordina
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 -
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 have
named input.g_rms. write the group number in this file. In
> > your shell script after command line write 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 a
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...
Inst
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
>
>
> On 11/22/12 5:44 AM, Kiwoong Kim wrote:
>
>> Hi,
>>
find forcefield 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
n 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/
Sog
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 coefficie
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