Dear Peter,
I appreciate your explanation :)
Regards,
Shima
- Original Message -
From: Peter C. Lai
To: Shima Arasteh
Cc: Discussion list for GROMACS users
Sent: Saturday, June 30, 2012 8:57 PM
Subject: Re: [gmx-users] Berger lipid
323 is proper for a higher melting point lipid
cerely,
> Shima
>
>
> - Original Message -
> From: Peter C. Lai
> To: Shima Arasteh ; Discussion list for GROMACS
> users
> Cc:
> Sent: Friday, June 29, 2012 2:54 PM
> Subject: Re: [gmx-users] Berger lipid
>
> yes
> http://www.frontiersin.org/B
that their study was done in
mammalian cells. Is this the reason of this T? They mean 37 centigrades. Right?
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Saturday, June 30, 2012 7:15 PM
Subject: Re:
On 6/30/12 11:03 AM, Shima Arasteh wrote:
Thanks Justin.
Yes, you are right. You wrote the tutorial for DPPC and I know that.
ok, I saw the temperatures upper than 271 K is proper for POPC. It's acceptable that 310
mentioned in Peter's paper is correct. But I'm wondering how they chose "310"
e, he explains that their study was done in
mammalian cells.
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Saturday, June 30, 2012 7:15 PM
Subject: Re: [gmx-users] Berger lipid
On 6/30/12 10:33 AM, Sh
in advance
Sincerely, Shima
- Original Message - From: Peter C. Lai To: Shima
Arasteh ; Discussion list for GROMACS users
Cc: Sent: Friday, June 29, 2012 2:54 PM Subject: Re:
[gmx-users] Berger lipid
yes
http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061
ers are not the same as your system . Would you telling me about the
reason of 310 K?
Thanks in advance
Sincerely,
Shima
- Original Message -
From: Peter C. Lai
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, June 29, 2012 2:54 PM
Subject: Re: [gmx-user
Dear Peter,
Thanks a lot :)
Sincerely,
Shima
- Original Message -
From: Peter C. Lai
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, June 29, 2012 2:54 PM
Subject: Re: [gmx-users] Berger lipid
yes
http://www.frontiersin.org
er
>
>
>
>
> Sincerely,
> Shima
>
>
>
> From: Peter Lai
> To: Discussion list for GROMACS users
> Sent: Friday, June 29, 2012 7:14 AM
> Subject: RE: [gmx-users] Berger lipid
>
> Uh didn't we go through all of thi
Dear Thomas,
It's a good idea. Thanks :)
Sincerely,
Shima
- Original Message -
From: Thomas Piggot
To: Discussion list for GROMACS users
Cc:
Sent: Friday, June 29, 2012 1:39 PM
Subject: Re: [gmx-users] Berger lipid
Hi Shima,
The lipids.rtp file in the charmm36.ff folder has
t for GROMACS users
Subject: Re: [gmx-users] Berger lipid
On 6/28/12 8:54 PM, Shima Arasteh wrote:
Yes, I know that as studied the Kalp15 tutorial.
Sorry, the last question :)
:
DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it ok?
Because I see that POPC.itp is also require
: [gmx-users] Berger lipid
Uh didn't we go through all of this like more than a month ago? I published a
paper using C36 POPC and even a linked to my popc.itp for it on this list...
Of course Shima is welcome to pdb2gmx his own POPC, which I am fairly certain
will result in an identical
ckage in lipidbook too.
Thanks Peter
Sincerely,
Shima
From: Peter Lai
To: Discussion list for GROMACS users
Sent: Friday, June 29, 2012 7:14 AM
Subject: RE: [gmx-users] Berger lipid
Uh didn't we go through all of this like more than a month ago? I p
__
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Thursday, June 28, 2012 7:56 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Berger lipid
On 6/28/12 8:54 PM, Shima Arasteh wrote:
> Y
[gmx-users] Berger lipid
On 6/28/12 8:54 PM, Shima Arasteh wrote:
> Yes, I know that as studied the Kalp15 tutorial.
> Sorry, the last question :)
> :
>
>DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it
> ok? Because I see that POPC.itp is also req
On 6/28/12 8:54 PM, Shima Arasteh wrote:
Yes, I know that as studied the Kalp15 tutorial.
Sorry, the last question :)
:
DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it ok?
Because I see that POPC.itp is also required for simulation of protein in
bilayer.
You ne
Message -
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Friday, June 29, 2012 5:16 AM
Subject: Re: [gmx-users] Berger lipid
On 6/28/12 8:43 PM, Shima Arasteh wrote:
>
>
> Yes, I have studied the article by Jeffery B. Klauda and other articles
> re
On 6/28/12 8:43 PM, Shima Arasteh wrote:
Yes, I have studied the article by Jeffery B. Klauda and other articles related
to C36. And know where the parameters of CHARMM36 were derived.
By the way, when I search the lipidbook to find the .itp file I can't find it! What about
the lipid .itp
orial it's written
"lipid.itp - Berger lipid parameters" )
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Friday, June 29, 2012 4:58 AM
Subject: Re: [gmx-users] Berger lipid
On 6/28/12 8:23 PM, Shima Ara
On 6/28/12 8:23 PM, Shima Arasteh wrote:
Thanks.
Yes, you told me this before CHARMM36 is better than CHARMM27. But I'm afraid
of using C36. Because I think it's a newer FF and and less studies have done
by it. Then if I face a problem, I can't find a way through articles!
Don't you think s
ima
- Original Message -
From: Justin A. Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, June 29, 2012 4:46 AM
Subject: Re: [gmx-users] Berger lipid
On 6/28/12 8:15 PM, Shima Arasteh wrote:
> Hi all,
>
> I want to simulate a protein in POPC b
On 6/28/12 8:15 PM, Shima Arasteh wrote:
Hi all,
I want to simulate a protein in POPC bilayer by CHARMM27 FF. I know
phospholipids and protein are defined well in CHARMM27. Is Berger lipid
required ?
No, these are different force fields entirely. The CHARMM36 parameter set is
better for
Hi all,
I want to simulate a protein in POPC bilayer by CHARMM27 FF. I know
phospholipids and protein are defined well in CHARMM27. Is Berger lipid
required ?
Thanks for your replies in advance.
Sincerely,
Shima
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