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

XAvier Periole x.periole at rug.nl
Mon Sep 16 15:55:23 CEST 2013


well … 

You might have guest yourself that dropping the particle decomposition is a problem for me since I took the time to fill up a report on a bug that I explain quite substantially how and why it was a problem.

pd remains the only manner to run a system with unusual bonded terms that span a large part of the box. dd and dlb simply do not go through and there is then no way to run the system. 

I used pd in a few application where the relative orientation of proteins were restrains using distance, angle and dihedral angles. the restrains were subsequently treated using a 6d-wham algorithm to obtain the PMF … I guess this won't be possible anymore … very very very sad!

While using coarse grain model pd was also often the only solution to run a system during the equilibration. It was never clear why but non-equilibrated system have severe trouble to run using dd. 

to conclude removing particle decomposition is a disaster.


On Sep 10, 2013, at 10:35 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
> The near-silence has been deafening, so these issues are regarded as
> closed. Anybody wanting a significant deviation from that plan will
> find the onus on them to do the work! :-)
> Cheers,
> Mark
> On Wed, Aug 14, 2013 at 5:06 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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