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

[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
> <gianluca at u.washington.edu> 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
> kind of usage in mind, and (for example) will issue a fatal error
> whenever that seems right. This will also kill the calling program,
> which is usually unacceptable. There's a current thread on gmx-users
> asking about library-type functionality, too. Better behaviour isn't
> likely to happen until someone steps up to make the code changes. So
> far it's not a priority for anyone who knows the code well enough to
> do it, and the learning curve too daunting for everyone else! :-)
>
> One doesn't have to hit disk with output files, either. Memory-mapped
> files and named pipes can be useful.
>
> Mark
>
>> I wonder if I can find more documentation about this topic.
>>
>> There is a python wrapper for gromacs functions here:
>>
>> http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/
>>
>> and a thread in the developers discussion:
>>
>> http://lists.gromacs.org/pipermail/gmx-developers/2009-March/003179.html
>>
>> Gianluca
>>
>>
>> On Sat, 31 Aug 2013, Justin Lemkul wrote:
>>
>>>
>>>
>>> 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_LIBS=ON There
>>>>> is no
>>>>> library called libmdrun.so like the one used in grompy. Could it be that
>>>>> libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command
>>>>> mdrun
>>>>> call libmd.so?
>>>>>
>>>>
>>>> I have never heard of anything called "libmdrun.so" and I do not see one
>>>> in any
>>>> of my current installations - 4.0.7, 4.5.5, or 4.6.3.  The mdrun command
>>>> should
>>>> be linked against libmd.so; you can check with ldd.
>>>>
>>>
>>> A quick look through the GromPy documentation suggests that libmdrun.so is
>>> something that GromPy creates through one of its scripts.  Having never used
>>> GromPy, that's the best I can offer.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>
>>> ==================================================
>>> --
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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
>> -----------------------------------------------------
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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
-----------------------------------------------------