Just to confirm what Jason said, there is no 3D-RISM support in Sander yet. We are still trying to work around the licensing issues with FFTW. You can using rism3d.snglpnt to do single point calculations and trajectory analysis. It is also possible to write NAB programs to do minimization and MD with 3D-RISM and there are some basic examples in AmberTools/tests/nab/ to get you started. However, there is no multiple time step support in NAB, so MD will be extremely slow.
Tyler
On 2013-02-05, at 2:16 PM, Jason Swails wrote:
> A couple comments:
>
> strings in Fortran namelists (like file names) need to be in single quotes,
> I believe. (Or double quotes, but some kind of quotes).
>
> Also, I don't think sander.RISM is actually released due to license issues
> with fftw -- I think you need to go through the NAB interface (see
> rism3d.snglpnt).
>
> HTH,
> Jason
>
> On Tue, Feb 5, 2013 at 2:05 PM, WenJuan Huang <hwjamber.gmail.com> wrote:
>
>> Hello all,
>>
>> I am trying to use 3d-rism calculation to obtain solvation thermodynamic
>> energies. In amber manual, it gives key words to irism settings. However,
>> the sample is not clear about the input file for this type of calculations.
>>
>> I tried to follow the sample in the manual like this:
>> &cntrl
>> imin = 1,
>> maxcyc = 200,
>> drms=1e-3,
>> ntmin=3,
>> ntpr=5,
>> ntb = 0,
>> cut = 999.0,
>> irism = 1
>> /
>> &rism
>> tolerance=1e-11,
>> solvcut=9999,
>> centering=2
>> /
>> END
>>
>> and also tried the input file like this by simply add irism key to a
>> general energy calculation input:
>> &cntrl
>> imin = 1,
>> ncyc = 1,
>> maxcyc = 1,
>> igb = 5, saltcon=0.2,
>> ntb = 0,
>> gbsa = 2,
>> cut = 999.0,
>> irism = 1
>> /
>> &rism
>> xvvfile=SPC_NaCl.xvv,
>> closure=KH,
>> asympcorr = F
>> solvcut=999.0,
>> tolerance=1e-11,
>> centering=-2,
>> nptrism=1,
>> ntwrism=1,
>> volfmt='DX',
>> write_thermo=1
>> /
>> END
>>
>> Both of them gave me "error in reading namelist cntrl". Could you please
>> help me check which part is wrong? Thanks a lot for your help!
>>
>> WenJuan Huang
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
________________________________________________________________
Tyler Luchko
Postdoctoral Associate
Case Group
BioMaPS Institute
Rutgers University
Piscataway, New Jersey
tluchko.rutgers.edu
848-445-5239
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Received on Tue Feb 05 2013 - 12:00:04 PST
