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

2013-08-31 Thread Gianluca Interlandi
Dear Mark, Thank you very much for the enlightment. I will look into named pipes. This might be appropriate since I'm calling mdrun from a TCL script in VMD. Gianluca On Sun, 1 Sep 2013, Mark Abraham wrote: On Sat, Aug 31, 2013 at 9:33 PM, Gianluca Interlandi wrote: Thanks for looking in

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

2013-08-31 Thread Mark Abraham
On Sat, Aug 31, 2013 at 9:33 PM, Gianluca Interlandi wrote: > Thanks for looking into that. I wonder whether routines of libmd.so can be > called directly from a python script just like grompy calles routines from > libmdrun.so One could do so, but the GROMACS "libraries" are not built with this

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

2013-08-31 Thread Gianluca Interlandi
Thanks for looking into that. I wonder whether routines of libmd.so can be called directly from a python script just like grompy calles routines from libmdrun.so I wonder if I can find more documentation about this topic. There is a python wrapper for gromacs functions here: http://sbcb.bioch

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

2013-08-31 Thread Justin Lemkul
On 8/31/13 3:11 PM, Justin Lemkul wrote: On 8/31/13 3:04 PM, Gianluca Interlandi wrote: I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LI

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

2013-08-31 Thread Justin Lemkul
On 8/31/13 3:04 PM, Gianluca Interlandi wrote: I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no library called libmdrun.so

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

2013-08-31 Thread Gianluca Interlandi
I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no library called libmdrun.so like the one used in grompy. Could it be that

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

2013-08-31 Thread Justin Lemkul
On 8/31/13 2:32 PM, Gianluca Interlandi wrote: Thanks Justin. I have been wondering where I can find all options of cmake (./configure --help used to print all possible options, whereas cmake --help prints out just the usage of cmake itself). There's nothing like this that I'm aware of, but

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

2013-08-31 Thread Gianluca Interlandi
Thanks Justin. I have been wondering where I can find all options of cmake (./configure --help used to print all possible options, whereas cmake --help prints out just the usage of cmake itself). Gianluca On Sat, 31 Aug 2013, Justin Lemkul wrote: On 8/31/13 2:16 PM, Gianluca Interlandi w

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

2013-08-31 Thread Justin Lemkul
On 8/31/13 2:16 PM, Gianluca Interlandi wrote: 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

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

2013-08-31 Thread 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