Dear Matias,
Not a silly question at all! I have just checked it, and there doesn't appear to be any gaps or spaces between the lipids in the periodic images, so I don't know if "excessive" space is an issue, but it is helpful eliminating one possibility!
Cheers,
Amanda
________________________________
From: Matias Machado <mmachado.pasteur.edu.uy>
Sent: 04 June 2020 00:51
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use?
Dear Amanda,
A very silly question, have you checked the PBC condition before running the simulation? I mean, have you visualized the periodic images of the membrane before any simulation?
I don't know how CHARMM-GUI prepares the system for running in AMBER code, but there are some issues when setting the periodic box in LEAP for membranes which leads to "excessive" space between lipids of neighboring images breaking the continuity of the membrane. That kind of issue may create odd behaviors at edges...
Hope it helps...
Matias Machado
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Batuhan Kav" <bkavlist.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Miércoles, 3 de Junio 2020 10:44:06
Asunto: Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use?
Hello,
I don’t have access to the data anymore but I remember that MC barostat, at least in case of lipid bilayers, had issues with properly equilibriating the structure. If I recall correctly, for instance, that the xy-dimensions of the box didn’t change considerably from the initial values and the area per lipid values did not converge. I think using Berendsen barostat with the semi-isotropic coupling solved most of these problems. After the structure is equilibrated , one can switch back to the MC barostat if desired.
I’m not sure if this will solve the problem but could be worth giving it a try.
Best,
Batuhan
> On 3 Jun 2020, at 15:17, David A Case <david.case.rutgers.edu> wrote:
>
> On Wed, Jun 03, 2020, Dave Cerutti wrote:
>
>> If you could provide a link to the archive where that advice is found, I
>> might be able to comment more, but for now I looked through the manual and
>> found the "baroscalingdir" keyword, which is there to control the
>> directions along which the box stretches during constant pressure
>> dynamics. This keyword is applicable with the Monte-Carlo barostat and
>> anisotropic pressure control. Since semi-isotropic is just a special case
>> of anisotropic, I don't see a reason you cannot combine ntp=3 and
>> barostat=2. The detailed balance condition on the MC barostat is
>> important, so someone may have made a note of DtB considerations if the box
>> does not stretch isotropically. However, if baroscalingdir can be an
>> option, any caveats are either solved or at least one person who programmed
>> the MC barostat thinks it's OK.
>>
>>>
>>> I've also read, back in the Amber forums, that when you use ntp=3, you
>>> should use barostat=1. Is this true?
>>>
>
> Please check with Prof. Wonpil Im at Lehigh University. I think I
> remember that he has looked at this problem, but I'm not sure if this
> has been published. Other Amber users running membrane simulations with
> Amber force fields and the MC barostat might want to comment on their
> experience.
>
> ....dac
>
>
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Received on Wed Jun 03 2020 - 18:00:02 PDT
