Lemkul
> Sent: Friday, 17 August 2012 12:33 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Protein-POPC bilayer
>
>
>
> On 8/16/12 10:21 PM, Mark Abraham wrote:
> > On 17/08/2012 11:46 AM, Justin Lemkul wrote:
> >>
> >>
> >&
:-)
Thanks Peter.
Sincerely,
Shima
- Original Message -
From: Peter C. Lai
To: Shima Arasteh
Cc: Discussion list for GROMACS users
Sent: Friday, August 17, 2012 8:48 AM
Subject: Re: [gmx-users] Protein-POPC bilayer
On 2012-08-16 09:04:35PM -0700, Shima Arasteh wrote
d before, if the box vectors and area per lipid
are in equilibrium by the end of the equilibration, you should be fine.
>
>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Peter C. Lai
> To: Shima Arasteh
> Cc: Discussion list for GROMACS users
&
Thanks for all explanations.
Sincerely,
Shima
- Original Message -
From: Peter C. Lai
To: Shima Arasteh
Cc: Discussion list for GROMACS users
Sent: Friday, August 17, 2012 8:19 AM
Subject: Re: [gmx-users] Protein-POPC bilayer
Can't remember why I said that, since it's not what I
to the consensus value of around 63–65Å per headgroup.
>
> This is where I asked the question about.
>
> Thanks.
>
>
>
>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Peter C. Lai
> To: Shima Arasteh ; Discussion list for GROMACS
&
ma Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, August 17, 2012 7:17 AM
Subject: Re: [gmx-users] Protein-POPC bilayer
Here is my MDP file I use for POPC work for NPT-after-NVT equilibration,
in caes you lost it from the time before:
You can choose to use V-rescale and Berendsen if you wa
: Friday, 17 August 2012 12:33 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Protein-POPC bilayer
>
>
>
> On 8/16/12 10:21 PM, Mark Abraham wrote:
> > On 17/08/2012 11:46 AM, Justin Lemkul wrote:
> >>
> >>
> >> On 8/16/12 9:
Here is my MDP file I use for POPC work for NPT-after-NVT equilibration,
in caes you lost it from the time before:
You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/
Parinello-Rahman with the paraeters below was stable for me with 238 POPC
and 21524 water.
integrator
On 8/16/12 10:21 PM, Mark Abraham wrote:
On 17/08/2012 11:46 AM, Justin Lemkul wrote:
On 8/16/12 9:43 PM, Jianguo Li wrote:
What I think is that anisotropic coupling may be faster in equilibrium. Suppose
the protein is quite different in x and y dimensions, after insertion, I think
it is fa
You always use semi-isotropic for bilayer work. The Z is decoupled from x-y
due to symmetry.
I don't think I mention anything differently in the paper.
Pcoupltype = semiisotropic
On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote:
>
> Hi,
>
> I have a question about the Prote
On 17/08/2012 11:46 AM, Justin Lemkul wrote:
On 8/16/12 9:43 PM, Jianguo Li wrote:
What I think is that anisotropic coupling may be faster in
equilibrium. Suppose
the protein is quite different in x and y dimensions, after
insertion, I think
it is faster to get equilibrium the box length sepa
On 8/16/12 9:43 PM, Jianguo Li wrote:
What I think is that anisotropic coupling may be faster in equilibrium. Suppose
the protein is quite different in x and y dimensions, after insertion, I think
it is faster to get equilibrium the box length separately. I agree with you that
semi-isotropic c
the job, but I expect it may take longer
time to reach equilibrium.
--Jianguo
From: Justin Lemkul
To: Jianguo Li ; Discussion list for GROMACS users
Sent: Friday, 17 August 2012, 9:19
Subject: Re: [gmx-users] Protein-POPC bilayer
On 8/16/12 9:14 PM
On 8/16/12 9:14 PM, Jianguo Li wrote:
After inserting the protein, the equilibrium box length in the x and y
dimension should be different, so you need anisotropic pressure coupling during
the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so
you can use semi-isotropic
From: Shima Arasteh
To: Discussion list for GROMACS users
Sent: Friday, 17 August 2012, 7:26
Subject: [gmx-users] Protein-POPC bilayer
Hi,
I have a question about the Protein-POPC system:
To insert a protein in lipid bilayer, I am suggested to simulate POPC in water
separately
Hi,
I have a question about the Protein-POPC system:
To insert a protein in lipid bilayer, I am suggested to simulate POPC in water
separately before insertion, it might decrease the time of final simulation.
It's OK!
In the article suggested me by dear Peter C. Lai, I read that POPC was
sim
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