Hi Magdalena,
Jason is right about the licensing issues with FFTW. We hope to sort this out and distribute sander.RISM but I'm not sure when this will be.
In the mean time 3D-RISM does work with NAB with identical keywords and almost identical features to sander.RISM. In NAB you cannot run multiple time step MD but the parallelism is more flexible, especially for small molecules. Sander limits the number of processes to the number of residues in the system but NAB does not. There are a few examples to get you started in $AMBERHOME/AmberTools/test/nab.
3D-RISM functionality is automatically built into NAB when you build the serial version of AmberTools. For the parallel version, set XFLIBS and include '-rismmpi' when you configure.
Tyler
On 2010-11-12, at 2:12 PM, Jason Swails wrote:
> Hello,
>
> Per a previous post on this list by Tyler (I'm having trouble locating it
> right now), I think there's a license issue preventing sander.RISM to be
> built, since it uses fftw which operates under the GPL -or- a paid
> commercial license. The GPL (unlike the LGPL) requires that any software
> that incorporates the source code of a GPLed project itself be open source,
> which sander is not. (The LGPL does not have this restriction).
>
> For this reason, RISM is only available in Amber through nab.
>
> I hope this helps,
> Jason
>
> On Fri, Nov 12, 2010 at 12:40 PM, Magdalena Gruziel <M.Gruziel.icm.edu.pl>wrote:
>
>>
>> Hello,
>>
>> i'd like to test rism but it seems, i do not
>> know how to congigure or compile the sources
>> to get it.
>> Whatever I try [also including XTRA_FLIBS and
>> -rismmpi option for the parallel version] no
>> sander.RISM/sander.MPI.RISM binaries get created.
>>
>> As I understood. rism1d binary is sth different
>> than sander.RISM [the latter being for 3d-rism, yes?]
>>
>> Should it be perhaps compiled separately?
>> does anyone know?
>> i would be very grateful for any hints..
>>
>> best regards
>> magdalena
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Fri Nov 12 2010 - 11:30:06 PST
