Hi David,
The only thing I found in the Amber mailing list archive was the link here:
http://archive.ambermd.org/201704/0072.html
In the middle, when the input file is given, it says to use barostat=1 with ntp=3 in the comments section. I'm unsure why this would be, and unsure why you can't use barostat=2 with ntp=3. I may go with what Batuhan suggested and use the Berendsen theromostat for equilibration with CHARMM, but let me know if you think this is a mistake!
Cheers,
Amanda
________________________________
From: David Cerutti <dscerutti.gmail.com>
Sent: 03 June 2020 18:29
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use?
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.
Dave
On Tue, Jun 2, 2020 at 11:55 PM Amanda Buyan <Amanda.Buyan.anu.edu.au>
wrote:
> Hi everyone,
>
> Thanks for your help on the Steered MD question before - it helped!
>
> I am also looking at running some simulations using the CHARMM36m
> forcefield in Amber. I've created my system on the CHARMM-GUI website,
> downloaded and ran the system by minimizing, heating and then relaxing
> restraints. When I get to the relax restraints file, however, the lipid
> bilayer is behaving strangely, in that it's curving slightly upwards at the
> corners! I'm sure this is not supposed to happen, so I was wondering if
> all of you can help clear something up for me.
>
> I'm currently running with the following:
>
> ---------
> ntp=3
> ninterface=2
> csurften=3
> gamma_ten=0.0
> barostat=2
> taup=1
> ---------
>
>
> I've also read, back in the Amber forums, that when you use ntp=3, you
> should use barostat=1. Is this true?
>
>
> Many thanks in advance for your help,
>
> Amanda
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 03 2020 - 17:30:01 PDT
