er, every problem begins to
> > resemble a nail.
> >
> >
> >
> > *From:* gmx-users-boun...@gromacs.org
> > [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Javier Cerezo
> > *Sent:* Friday, 3 December 2010 2:46 AM
> > *To:* gmx-users@groma
ubject:* Re: [gmx-users] Re: individual lateral diffusion coefficients
Sorry for the misspell...
Thanks Justin.
Do you *know* the reason behind?
I am trying following that protocol and my P curve in not as linear as
All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding
the
s-boun...@gromacs.org] On
Behalf Of Javier Cerezo
Sent: Friday, 3 December 2010 2:46 AM
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Re: individual lateral diffusion coefficients
Sorry for the misspell...
Thanks Justin.
Do you know the reason behind?
I am trying following that protoc
Dear Javier, Justin, Xavier...
Thank you very much for your feedback. Finally I decided to create a
group for each PO4 in my system and calculate all the individual
diffusion values. I also plotted all the MSDs as a function of time and
took a safe -beginfit -endfit interval for the fittings. I thi
Dear Angel,
I agree with Justin comments and I might add:
Taken from the marrink-2004JPC martini paper:
"Microsecond simulations of the bilayer containing 256
DPPC molecules allows the observation of truely long
time diffusive behavior. At T = 323 K, the lateral diffusion
rates of DPPC equals 3
Javier Cerezo wrote:
Thanks Justin.
Do you the reason behind?
I am trying following that protocol and my P curve in not as linear as
All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding
the linear region, the slopes are not the same. So which one do you
think is more accur
Sorry for the misspell...
Thanks Justin.
Do you *know* the reason behind?
I am trying following that protocol and my P curve in not as linear as
All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding
the linear region, the slopes are not the same. So which one do you
think is
Thanks Justin.
Do you the reason behind?
I am trying following that protocol and my P curve in not as linear as
All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding
the linear region, the slopes are not the same. So which one do you
think is more accurate?
Thanks again
Jav
Ángel Piñeiro wrote:
Hi Javier
I think I saw this in several mails of this list and it is also implicit
in the Justin tutorial for analysis of bilayers. I am not sure whether
or not this has also been published... I do not remember any paper. I
think this is reasonable for lipids in contact
Hi Javier
I think I saw this in several mails of this list and it is also implicit
in the Justin tutorial for analysis of bilayers. I am not sure whether
or not this has also been published... I do not remember any paper. I
think this is reasonable for lipids in contact with membrane proteins
becau
Hi Ángel
Can you provide a citation about the use of only PO4 atoms to calculate
the diffusion constant? Is it always recommended or just with CG
simulations? I'm also working on diffusion calculation and that will be
interesting.
By the way, regarding the index files I mentioned, it might b
Hi Javier
1.- you are right! the diff_mol.xvg file I reported was from a previous
attempt in which I used the whole lipid molecules with the -mol option
on, instead of the PO4 beads with -mol off. Sorry for this confusion
2.- As I said above, I did attempts using both the whole molecule and
the PO
Hello Ángel.
Well, there are a some things that I don't understand about your
calculation, but might be just a problem of mine. Here you have my comments:
1. How do you get the diff_mol.xvg file if you are not using -mol in
your command line input (and you index file has broken molecules).
I want to add that the MSD as a function of time (msd.xvg file) looks
completely linear
Greetings,
Ángel Piñeiro.
On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote:
> Dear all,
> I aim to calculate the lateral diffusion coefficients of lipids as a
> function of the distance to a membrane p
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