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

[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.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
-----------------------------------------------------