[gmx-users] compilation of g_hbond after bugfix

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 17 07:54:10 CEST 2011

On 17/05/2011 3:40 PM, bipin singh wrote:
> Hello,
> I want to compile the source code gmx_hbond.c after the below
> mentioned bugfix, I have already installed gromacs 4.5.3, how can I
> compile only gmx_hbond.c in already installed
> gromacs 4.5.3.

If you've built using configure, then there is no way to do this. Just 
do a normal "make install" and if you have modified the source file, 
make will work out what to do. You may wish to rename the old executable 
before you do this, so that you can still access both versions.

If you've built using CMake, then make g_hbond should work.


>> Hi,
>> There have been reports about inconsistencies between older (<= 4.0.7?) and newer versions of g_hbond, where the older seem to have been more reliable. I found and killed the bug>that caused the newer versions to miscount the hbonds. Checkout release-4-5-patches to get the bugfix, or patch it yourself by commenting out line 1497, which reads "return hbNo;":
>>    if (bBox){
>> if (d>a&&  bMerge&&  (bContact || isInterchangable(hb, d, a, grpd, grpa))) { /* acceptor is also a donor a\
>> nd vice versa? */
>>             /* return hbNo; */
>> daSwap = TRUE; /* If so, then their history should be filed with donor and acceptor swapped. */
>>        }
>> Simple as that

More information about the gromacs.org_gmx-users mailing list