[gmx-users] Regarding the comparison of two result

[Justin Lemkul]

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

-- 
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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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