[gmx-users] plans for mdrun features to deprecate in GROMACS 5.0

[Mark Abraham]

On Wed, Aug 14, 2013 at 10:17 PM, rajat desikan <rajatdesikan at gmail.com> wrote:
> I am interested in Generalized Born. My coding skills are limited, but I
> would like to help to whatever extent I can.

Big issues at the moment are that both the "all vs all" and
SIMD-accelerated GB kernels are broken in 4.6.x but worked in 4.5.x
(see http://redmine.gromacs.org/issues/1249). That probably means that
performance of the plain-C kernels is lower than a similar
explicit-solvent system. I expect that the problem is not severe -
just that some assumption in the GB kernel or setup code has been
violated during the changes leading to 4.6. If you're keen, those
would be useful things to have working!

> I am also interested in helping towards revamping the tutorials if the need
> should arise.

There are several tutorials under preparation for the GROMACS workshop
in Virginia in September. I'm sure some preliminary feedback on those
would be welcome when they're ready!

Thanks!

Mark

> On Wed, Aug 14, 2013 at 8:36 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> Hi gmx-users and gmx-developers,
>>
>> There are a number of features of GROMACS that we plan to drop for 5.0
>> (scheduled for early 2014). We don’t like doing this, but if things
>> are broken or cause developers pain, then they will go unless there is
>> manpower to support them. We’d like to keep you informed and hear how
>> much pain any of this might cause. Some features will be dropped
>> entirely, and others are likely to be reduced to explicit support only
>> for some cases. Some discussion has already occurred here
>> http://redmine.gromacs.org/issues/1292.
>>
>> Things we plan to drop entirely:
>> * particle decomposition (see below)
>> * current QM support (this will be dropped, work on a replacement is
>> underway, planned for 5.0)
>> * writing of pair distance and/or time-averaged pair distance to
>> energy files during simulations with position/orientation restraints
>> * reaction-field-nec
>> * Encad-shift
>> * mdrun -ionize
>> * GCT
>> * mdrun -seppot
>> * mdrun -ffscan
>> * OpenMM support
>>
>> There are several algorithms (e.g. fancy kinds of restraints) that
>> have only ever worked with particle decomposition (if they work at
>> all...). We plan to support these only in serial.
>>
>> Things that will likely only work in serial (ie. single-domain DD):
>> * ensemble- and time-averaged distance restraints
>> * L-BFGS energy minimization
>> * Generalized Born
>>
>> In some cases, “in serial” might mean “in parallel (with DD) with an
>> extra communication stage that will make it work, but might scale
>> poorly.” Or “in parallel but if things diffuse too far, the simulation
>> will crash.” If you have working examples of any of the above in
>> parallel, we would be most interested to hear from you. We’d like to
>> construct test cases that show what works now, so that later if we are
>> able to support some kind of parallelism, we can show that it still
>> works.
>>
>> Things that won’t support constraints (because the implementations are
>> broken or missing):
>> * L-BFGS energy minimization
>> * MTTK pressure coupling
>>
>> As always, what goes into GROMACS depends on people putting the work
>> in. If something above would affect you, then do speak up.
>> Contributions of working test cases are particularly valuable, but in
>> the end you might have to be the one to write the code to make the
>> test pass. You will have the option of continuing to use old code,
>> too!
>>
>> Cheers,
>>
>> Mark
>> --
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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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