Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use?

From: Amanda Buyan <Amanda.Buyan.anu.edu.au>
Date: Thu, 4 Jun 2020 00:15:01 +0000

Thanks David and Batuhan,

I'll check with Professor Wonpil Im about this. If he has published something on the subject, I'd be very grateful!

I can also try to run with the Berendsen barostat with ntp=3 and let you know how I go.


Cheers,

Amanda

________________________________
From: Batuhan Kav <bkavlist.gmail.com>
Sent: 03 June 2020 23:44
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use?

Hello,

I donít 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 didnít 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.

Iím 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 - 17:30:02 PDT
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