[gmx-users] grompy and how to call energy routine

[Gianluca Interlandi]

After reading a bit more in the grompy directory, I found that the file 
__init__.py loads the necessary libraries, e.g., mdrun.so. This is because 
gromacs (they use version 4.0.7) was compiled with the flag 
--enable-shared. I am using version 4.6.3 which uses "cmake" instead of 
"configure". Is there an equivalent flag for cmake that corresponds to 
"--enable-shared"?

Thanks,

      Gianluca

On Sat, 31 Aug 2013, Gianluca Interlandi wrote:

> Hi!
>
> I am currently using "mdrun -rerun" in order to get the energy of a system to 
> be used in a Monte Carlo algortihm. A while ago, I was pointed to Grompy 
> which should be capable of performing Monte Carlo using gromacs libraries (my 
> description might not be very accurate here). I have downloaded grompy from 
> git but I cannot find my way through (sorry, I'm rusty with python).
>
> Is there a way how I can directly call the gromacs energy routine from python 
> and/or TCL? "mdrun -rerun" works but it creates overhead because the 
> conformation has to be written to disk, then read by mdrun which writes an 
> energy file that needs to be read by g_energy. I would like to have a library 
> that can be called from my TCL/python script.
>
> I would appreciate any help on this.
>
> Thanks,
>
>     Gianluca
>
> PS: According to the roadmap MC should be available in version 5.0 but until 
> it's released I need to find an alternative :)
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca at u.washington.edu
>                    +1 (206) 685 4435
>                    http://artemide.bioeng.washington.edu/
>
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
>                    http://healthynaturalbaby.org
> -----------------------------------------------------
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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
                     http://healthynaturalbaby.org
-----------------------------------------------------