[gmx-users] Modified Gromacs and OPENMM

[Szilárd Páll]

Hi,

> Thanks for the reply. The part I modified is the implicit solvent
> part, particularly the Still model. Also I modified a part of nonbonded
> kernel, not sse ones. So I assumed I have to link GROMACS with OPENMM
> using customGBforce?

You mean that you modified the CUDA kernel inside OpenMM, right? If
you did that than it should be as simple as recompiling OpenMM and
using this version to link against mdrun-gpu. However, as you suggest
you can use the CustomGBForce class to define a GB model in a  general
way. For that you should look at the OpenMM wrapper module (see
below). I'm not entirely sure what you mean so part of this is
guessing...

> Is there a guide of how currently GROMACS is linked to OPENMM?

That's "fairly" straightforward. In runner.c:mdruner(), when an
OpenMM-enabled mdrun-gpu is used, all function pointers in the
integrator[] array simply point to md_openmm.c:do_md_openmm() (which
is a stripped-down version of md.c:do_md()). This contains the main MD
loop which besides all the Gromacs-magic essentially does:

openmm_init();
while(!bLastStep) {
openmm_copy_state();
openmm_take_one_step();
}
openmm_cleanup();

Finally, all the logic of interfacing with OpenMM is implemented in
src/kernel/openmm_wrapper.cpp, so I think that should be pretty much
the only place where you need to modify things to use
additional/custom OpenMM functionality in Gromacs.

Cheers,
--
Szilárd

> On Fri, Apr 29, 2011 at 3:08 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> Chi-cheng Chiu wrote:
>>>
>>> Hi Gromacs users & developers,
>>> If I modified gromacs, will my modification works if I complied it with
>>> OPENMM and use GPU?
>>
>> Presumably, if you have written sound code that uses compatible functions
>> that are actually implemented in the OpenMM library, then yes.  If you want
>> a more specific answer, you'll have to be more specific about what "modified
>> Gromacs" actually means.
>>
>> -Justin
>>
>>> Thanks!
>>>
>>> Regards,
>>>
>>> Chi-cheng
>>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>