[gmx-users] Tutorial updates

[Justin Lemkul]

On 7/9/14, 2:40 PM, Oliver Stueker wrote:
> Hi Justin,
>
> Do you plan to keep the Gromacs 4.x versions of your tutorials (which by
> the way are excellent) around for a little longer as well?
>
>  From my experience It will still take quite some time until Gromacs 5 is
> available on most Clusters and Linux-package repositories, whereas the
> Gromacs 4 versions are readily available.
>

The old tutorials are (mostly) still available.  Just append "_old" to the URL 
for the tutorial title, e.g. "lysozyme_old" in place of just "lysozyme."  A 
couple of the tutorials I simply converted (vsites and biphasic) because there 
are so few steps (they are hardly "tutorials," just demonstrations) that there 
was no sense in making a "backup" for the old version.

Ultimately, the old versions will go away.  There's already a large amount of 
upkeep and user feedback to take care of, and I simply don't have time to keep 
track of multiple versions of things.

Additionally, anyone who has worked through any of the tutorials who would like 
to look through the new ones to make sure everything makes sense - feedback 
would be appreciated.  I'm basically just converting command syntax and updating 
.mdp files, but I'm not regenerating all of the data, so if anything is going 
haywire, I don't know yet :)

-Justin

>
> Best,
> Oliver
>
>
>
> On Mon, Jul 7, 2014 at 7:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> All,
>>
>> For anyone using my tutorials, you will notice some changes in the coming
>> days.  I am updating all of them to be compatible with the newly released
>> Gromacs version 5.0.  Most of these changes will be superficial, such as
>> small changes to command names or options.  I have already updated all of
>> the tutorials except the ones related to free energy calculations, since
>> these will require the greatest amount of work given the changes in .mdp
>> options.
>>
>> Be advised that content will be somewhat fluid over the next few days, as
>> I find time to make the necessary changes.  Feedback on clarity and
>> correctness is always welcome.
>>
>> -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.
>>

-- 
==================================================

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

==================================================