[gmx-users] Regarding the comparison of two result

[rajat desikan]

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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> 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