[gmx-users] Regarding the comparison of two result

[rama david]

Dear friends,
      Thank you  Justin and Rajat for your suggestions.
I think it is really better to do all the MD in latest version or in the
same version.
That will avoid the unnecessary falls and critics.
With best regards,
Rama david


On Fri, May 2, 2014 at 6:13 PM, rajat desikan <rajatdesikan at gmail.com>wrote:

> I forgot to mention that the earlier simulations were with version 4.5.4
>
>
> On Fri, May 2, 2014 at 6:13 PM, rajat desikan <rajatdesikan at gmail.com
> >wrote:
>
> > Hi,
> > I would suggest caution. I had a DPPC bilayer interacting with organic
> > molecules (beta naphthol) which are supposed to alter the phase
> behaviour.
> > The initial simulations using group cutoffs didn't capture one region of
> > the experimental phase diagram, even with 200 ns of simulation (SLIPIDS +
> > GAFF). However, I am able to capture this phase with Verlet cutoffs in
> > version 4.6.4 in the high temperature range (Low temperature is
> problematic
> > due to kinetic trapping in all simulations). This is probably because the
> > Verlet cutoff scheme uses better model physics. So, make a cautious
> > decision before going ahead.
> >
> > Regards,
> >
> >
> > On Fri, May 2, 2014 at 5:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 5/2/14, 1:37 AM, rama david wrote:
> >>
> >>> Dear Friends,
> >>>
> >>>   I did MD simulation of two peptide that show that they form
> >>> antiparallel
> >>> beta sheet structure after 120 ns . i used gromacs 4.5.5 version.
> >>>                   presently  I completed MD simulation of another
> >>> peptide (
> >>> Different sequence). but I am using gromacs 4.6.3 . I found that two
> >>> peptide start to form anti parallelstructure around 15 ns.
> >>>                My question is that are this two result at all
> comparable
> >>> as
> >>> the version of software is diff. ?? is this result upto publication ???
> >>>
> >>>
> >>> I am looking forward for answer .
> >>> I know this is  a very simple but complicated to me.
> >>>
> >>>
> >> You'd have to look into the release notes to see if there were any
> >> relevant changes based on your run settings and such.  There were
> hundreds
> >> of changes between 4.5.5 and 4.6.3 - changing between release series
> can be
> >> a bit dicey. Changes within a release series should give consistent
> >> results, except in the case of critical bugs being fixed (i.e.
> everything
> >> in 4.5.x should match, everything in 4.6.x should match, but 4.5.x and
> >> 4.6.x may not necessarily be the same, depending on what the relevant
> >> changes were).  I would expect "standard" MD to probably be OK, but you
> >> really do need to look at all of the changes to determine if that's
> right.
> >>  Rule of thumb (at least, in my mind) - pick a version (the newest one
> >> available at the time, or whatever makes sense for scientific continuity
> >> with other ongoing or completed work) and stick with it.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 601
> >> 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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> >
> >
> >
> > --
> > Rajat Desikan (Ph.D Scholar)
> > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
> >
>
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
> --
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