[gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 115

Timofey Tyugashev tyugashev at niboch.nsc.ru
Sat Feb 20 07:24:52 CET 2016

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-request at maillist.sys.kth.se пишет:
> Message: 2
> Date: Fri, 19 Feb 2016 14:51:29 +0100
> From: Szil?rd P?ll<pall.szilard at gmail.com>
> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
> 	<gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] correct rlist and Verlet scheme
> Message-ID:
> 	<CANnYEw7tZTSNV4ZyZtmEH=5sVhHGU+VYiCn0Dy9yK3tc_9vAAw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> On Fri, Feb 19, 2016 at 1:23 PM, Timofey Tyugashev<tyugashev at 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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