[gmx-users] Important bugfix for g_hbond

Baofu Qiao qiaobf at gmail.com
Tue May 17 15:57:54 CEST 2011

Hi Erik and others,

After the bugfixed, I still have one problem: the average HB per SPC/E 
water is calculated to be ~1.8 in a pure water system from g_hbond, 
which has been previously reported to be 3.6 (Kumar, Schmidt & Skinner 
JCP, 2007, 126, 204107) . I have no idea where the difference comes 
from. Could you provide some help? Thanks a lot!

Some info:
4000 SPC/E water simulated at T=298K using NTP;
"Average number of hbonds per timeframe 7217.386 out of 8e+06 possible" 
was reported by (echo -e "SOL\nSOL"| g_hbond2 -f T298 -s T298 -n 
-merge). Note that the value of 7217 is independent of -merge/-nomerge.
I am using Gromacs 4.5.3 with your 'bugfix". Gromacs 4.0.7 give the 
similar value of about 7210 with -merge or -nomerge.

Any suggestion is appreciate!

Best wishes,
Baofu Qiao

On 05/10/2011 03:08 PM, Erik Marklund wrote:
> 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.

  Dr. Baofu Qiao
  Institute for Computational Physics
  Universität Stuttgart
  Pfaffenwaldring 27
  70569 Stuttgart

  Tel: +49(0)711 68563607
  Fax: +49(0)711 68563658

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