[gmx-users] grompy and how to call energy routine
mark.j.abraham at gmail.com
Sun Sep 1 00:37:35 CEST 2013
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
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.
> I wonder if I can find more documentation about this topic.
> There is a python wrapper for gromacs functions here:
> and a thread in the developers discussion:
> 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
>>>> 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
>>> 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 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
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> gmx-users mailing list gmx-users at gromacs.org
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