[gmx-developers] residue-residue interaction energies

aar2163 at columbia.edu aar2163 at columbia.edu
Mon Nov 18 23:01:45 CET 2013


I apparently solved my issue.

I redefined the gmx_grppairener_t structure on  
include/types/forcerec.h to have an additional rvec *avener.

To have grompp accept a higher number of energygrps I had to allocate  
every energygrps related variable with BIG_STRLEN instead of STRLEN in  
files src/gmxlib/readinp.c and src/kernel/readir.c and increase the  
value of MAXPTR in the latter file. I do not know if this could have  
weird effects, but everything is working fine in my machine with two  
different versions of gcc to compile it.


Quoting Mark Abraham <mark.j.abraham at gmail.com>:

> Scripting writing an .mdp file, running grompp, running mdrun -rerun,
> running gmxdump (or whatever) on the resulting .edr or .log file will solve
> your problem a hundred times faster than trying to extend the number of
> energy groups in mdrun. Whether that energy decomposition has a physical
> interpretation and this method will measure it is another thing!
> Mark
> On Fri, Nov 15, 2013 at 11:49 PM, <aar2163 at columbia.edu> wrote:
>> This is the second time I try to post this, but the first apparently did
>> not work. I apologize if you receive it twice.
>> Hi,
>> I want to calculate inter-residue non-bonded interaction energies between
>> all pairs of residues of a relatively large protein.
>> Since most of these will be zero and I just want average values, I do not
>> want to write the information to edr files. Furthermore, there seems to be
>> a limit on the number of energygrps allowed.
>> I'm going through the code of version 4.6.3 to try to make modifications
>> that solve my problem. My plan would be to have grompp accept an arbitrary
>> number of energygrps and mdrun -rerun store the values in a NxN matrix and
>> print non-zero averages to a custom output file. Any help on where to look
>> to accomplish any of this would be very welcome.
>> Thanks.
>> Andre.
>> --
>> gromacs.org_gmx-developers mailing list
>> gromacs.org_gmx-developers at maillist.sys.kth.se
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-developers-request at gromacs.org.

More information about the gromacs.org_gmx-developers mailing list