[gmx-users] Unstable Alpha Helix

[Mark Abraham]

Hi,

Yes of course lots of mdp parameters affect the quality of your model
physics. You should choose them carefully, in particular to align with how
your force field was parameterized, or is subsequently used (and shown to
work well). Offhand, the AMBER force fields are paramterized and used plain
cutoff VDW, so your use of potential-switch implements a model that is at
best doubtful until shown otherwise.

Mark

On Wed, Dec 21, 2016 at 9:16 PM <amitbehra at chemeng.iisc.ernet.in> wrote:

> Hello Justin,
> I am using "stride" program to analyze the helices.
> Can the Potential switch and other mdp parameters affect the stability of
> an Alphahelix.
>
> Regards,
> Amit
> > Date: Mon, 19 Dec 2016 08:06:29 -0500
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Unstable Alpha Helix
> > Message-ID: <78b951a1-4cb3-e4fc-4239-cc19fd03c9a5 at vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 12/19/16 7:01 AM, amitbehra at chemeng.iisc.ernet.in wrote:
> >> Hello everyone,
> >> I am trying to simulate an Alpha helix inside a bilayer. But a part of
> >> the
> >> alpha helix is loosing its form and converting into turns( while
> >> alphahelix should be stable in the bilayer environment)
> >
> > How are you assessing this?  DSSP?  Dihedral time series?  Note that
> > simple
> > visualization is often misleading.  Helices can still be helices, even if
> > the
> > program you're looking at disagrees.
> >
> > -Justin
> >
> >> I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer.
> >> I am using Potential-switch for VdW and PME for electrostatics.
> >> Does these parameters affect the form of the Alphahelix ?
> >>
> >> Regards,
> >> Amit
> >>
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> --
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