In this paper the following is used: "...All bonds were constrained
using the P-LINCS algorithm [42], allowing an integration time step of 2
fs..." for amber99sb-ildn.
On the other hand, isn't h-bond only constraints is the usual way for
AMBER? The papers for FFs say so. And I've seen recommendations on the
mailing list to constrain h-bonds only for AMBER or CHARMM.
I've seen the option for virtual sites, but entries for some DNA bases
are missing and so they are of no use to me now. Maybe I'll try it
sometime in the future with protein only model. Or if manage to build
the missing ones.
19.02.2016 19:51, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:
Message: 2
Date: Fri, 19 Feb 2016 14:51:29 +0100
From: Szil?rd P?ll<pall.szil...@gmail.com>
To: Discussion list for GROMACS users<gmx-us...@gromacs.org>
Cc: Discussion list for GROMACS users
<gromacs.org_gmx-users@maillist.sys.kth.se>
Subject: Re: [gmx-users] correct rlist and Verlet scheme
Message-ID:
<CANnYEw7tZTSNV4ZyZtmEH=5svhhgu+vyicn0dy9yk3tc_9v...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
On Fri, Feb 19, 2016 at 1:23 PM, Timofey Tyugashev<tyugas...@niboch.nsc.ru>
wrote:
>And here my hope for quick and easy solution hath end.
>All of the points you make ring true. Especially ones about software
>engineering and funding in science (or maybe I'm more familiar with them).
>
>Actually, ne relatively recent paper, "Phosphorylation of PPAR? Affects
>the Collective Motions of the PPAR?-RXR?-DNA Complex" (
>http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123984#sec008),
>uses AMBER99SB-ILDN with GROMACS 4.6 and Justin Lemkul is listed as the
>first author. And the simulated structure is a protein-DNA complex. So it
>should be very close to my case.
>The one thing that looks strange to me: both rvdw (LJ interacions) and
>box-solute distance set at 1.0 nm. Shouldn't the latter be larger to avoid
>probable periodic image interactions problems?
>Otherwise, looks like my settings are generally the same, except
>forgetting that LINCS allows 2fs step.
>
I guess you meant 4-5 fs*if* combined with virtual sites. At 2 fs you can
use h-bond only constraints if i) you prefer the resulting physics or ii)
you want to have a bit better performance and a lot better scalability.
--
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