Dear Vitaly Chaban
yes. my md simulation is equilibrioum.
I did simulation of protein-dna. I want to know how protein and dna close
together and interact together (approach of protein to major groove of dna).
thanks alot in advance.
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- Original Message -
From: leila karami
Date: Tuesday, June 29, 2010 18:08
Subject: [gmx-users] g_msd and diffusion coefficent
To: gmx-users@gromacs.org
> Dear Mark Abraham> No, I want to measure something about the diffusion of my
> protein to DNA (especially to major groo
Dear Vitaly Chaban
I know using index file but gromacs say : select only 1 group. what is this
group ? protein? or DNA?
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Dear Mark Abraham
No, I want to measure something about the diffusion of my protein to
DNA (especially to major groove of DNA) in the presence of water (as
solvent).
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- Original Message -
From: leila karami
Date: Tuesday, June 29, 2010 17:32
Subject: [gmx-users] g_msd and diffusion coefficent
To: gmx-users@gromacs.org
> Dear Mark Abraham > > yes. pr means protein. I want to obtain diffusion of
> protein within dna. I want to know
Dear Mark Abraham
yes. pr means protein. I want to obtain diffusion of protein within dna. I
want to know how/how much pr diffuse to dna.
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- Original Message -
From: leila karami
Date: Tuesday, June 29, 2010 16:41
Subject: [gmx-users] g_msd and diffusion coefficent
To: gmx-users@gromacs.org
> Hi gromacs users > > in my system, there are pr, dna, water and Na and I
> want to obtain diffusion of pr in dna bu
Hi gromacs users
in my system, there are pr, dna, water and Na and I want to obtain diffusion
of pr in dna but when I use g_msd command, gromacs says select only 1
group. should be this group pr or dna?
Thanks a lot in advance.
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leila karami wrote:
Hi gromacs users
I did simulation of pr-dna by gromacs. I want to obtain diffusion
coefficent of pr to dna. I raed manual (g_msd) in which there are
diffusion coefficent only for 1 and 2 dimension as follows respectively :
-type : Compute diffusion coefficient in one
Hi gromacs users
I did simulation of pr-dna by gromacs. I want to obtain diffusion coefficent
of pr to dna. I raed manual (g_msd) in which there are diffusion
coefficent only for 1 and 2 dimension as follows respectively :
-type : Compute diffusion coefficient in one direction: no, x, y or z
-l
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