[gmx-users] Regarding the comparison of two result

rajat desikan rajatdesikan at gmail.com
Fri May 2 14:43:28 CEST 2014

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.


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

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