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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