Hi,
What about reading an external file? It's already the case for distance
restraints for example.
Gerald.
On 01/22/2015 02:23 PM, Jason Swails wrote:
> On Thu, Jan 22, 2015 at 7:58 AM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>> On Thu, Jan 22, 2015, Jason Swails wrote:
>>>
>>> While sander and pmemd have a character limit on
>>> the length of the mask,
>>
>> Why don't we just change this?
>>
>
> We can increase the limit, but as long as we use Fortran namelists to
> supply sander/pmemd input, we will *always* need some sort of limit. [1]
> At the time, 256 characters probably seemed like a
> "too-large-to-ever-be-exceeded" safe limit :).
>
> The main thing I'm concerned about is MPI -- Amber likes to broadcast
> entire common blocks via the first element (which is perfectly fine), but
> changing the size of the individual items *in* the common blocks is a
> recipe for subtle bugs if you're not careful. (That said, I don't think the
> mds common block is broadcast from master to anywhere else, so this is
> probably an easy change).
>
>
>>
>> Larger update would be to allow multiple masks, with different restraint
>>
>> weights. We already allow multiple masks (through GROUP), so it's just a
>>
>> matter of coming up with a user interface that supports it.
>
>
> This would also be possible, but again, there will need to be arbitrary
> compile-time limits imposed on how *many* masks we allow. [1] I'm pretty
> sure I know where to make those changes, so I can draft a
> proof-of-principle change that implements the above, if you want.
>
> All the best,
> Jason
>
> [1] Fortran namelists do not allow dynamic *anything* in input -- all
> array/collection sizes must be fixed at compile time
>
--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
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Received on Thu Jan 22 2015 - 06:00:05 PST
