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

[Mark Abraham]

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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