Well, not everybody does MM with Amber...
G.
On 02/12/2014 10:46 PM, Scott Le Grand wrote:
> You *could* release AMBER 12 PMEMD as the new Sander.
>
> And then make AMBER 14 PMEMD invite-only featured.
>
> What's left in Sander that people crave for in PMEMD?
>
>
>
>
>
>
>
> On Wed, Feb 12, 2014 at 2:35 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> The problem is it's a victim of it's own success. People used to put stuff
>> in sander and if it was used a LOT it was migrated to pmemd. Now they want
>> to just put it straight in pmemd since to be honest if it's just in sander
>> its kind of useless these days.
>>
>> The problem is how to deal with this and yes I fully agree ALL of this
>> should have gone in over the last year. I vote once things are locked on
>> Friday we have at least another 6 weeks to work on cleaning up pmemd and
>> optimizing things ready for release. This may include gutting some stuff.
>> Otherwise yes we will just end up with a slow pmemd. :-(
>>
>> All the best
>> Ross
>>
>>
>> On 2/12/14, 2:13 PM, "Scott Le Grand" <varelse2005.gmail.com> wrote:
>>
>>> IMO PMEMD is reaching the point of collapse.
>>>
>>> There are way too many if/then clauses splattered all over the code with a
>>> disturbingly high number of them in inner loops.
>>>
>>> I am not going to be able to add many more features to the GPU codebase
>>> and
>>> I am beginning to consider splitting off from the main tree so that more
>>> control can be enforced on feature additions that will run on the GPU.
>>>
>>> Softcore TI is going to be a bear to get running efficiently. And it's
>>> hard for me to shake the feeling that the methodology is not quite ready
>>> for primetime. Add in EMIL, EMAP, and the remaining potpourri of
>>> potential
>>> features I hadn't heard of until the past few weeks and I'm reaching my
>>> limit here. Maybe it's time to deprecate and remove some stuff before
>>> this
>>> becomes Sander Mk II?
>>>
>>> Just my two cents...
>>>
>>> Scott
>>>
>>>
>>> On Wed, Feb 12, 2014 at 1:32 PM, David A Case
>>> <case.biomaps.rutgers.edu>wrote:
>>>
>>>> On Wed, Feb 12, 2014, Ross Walker wrote:
>>>>
>>>>> One thing I would like to avoid though as much as possible is people
>>>>> adding incomplete new methods to PMEMD. E.g. adding a new VDW
>>>> potential
>>>>> but not supporting IPS or GB. We shouldn't be doing this unless there
>>>> is
>>>> a
>>>>> real technical reason for not being able to do it.
>>>>
>>>> I agree, but would argue that we should *not* allow 12-6-4 and GB
>>>> together, since it (12-6-4) was never parameterized for that model, and
>>>> I
>>>> have a general bias against allowing (or at least, against encouraging)
>>>> explicit ions in GB simulations. I hope it's easy to catch that
>>>> combination and disallow it (in both sander and pmemd.)
>>>>
>>>> This could, of course, be revisted in future releases, if the
>>>> combination
>>>> is
>>>> demonstrated to be useful.
>>>>
>>>> On a related note, should we not remove (or #ifdef out) the "charge
>>>> relocation"
>>>> model? I don't think that has been well tested enough to support
>>>> publically. The clean thing to do would to make a new branch, then
>>>> remove
>>>> traces of this in the master.
>>>>
>>>> ...dac
>>>>
>>>>
>>>> _______________________________________________
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>>>>
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>>
>>
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--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
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e-mail : Gerald.Monard.univ-lorraine.fr
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Received on Wed Feb 12 2014 - 15:00:05 PST
