Hi,
It's a matter of how you count the hbonds. One water can participate in
four hydrogen bonds (sort of); two as an acceptor, and two as a donor.
But that leads to double counting of hbonds if we think that Nmax =
Nwater*4. Analogously: if a long line of people are connected by holding
hands, every person make two connections, but the total number of
connections divided by the number of poeople approaches one as the
number of people approaches infinity. Note how in the case of your hbond
calculations 1.8*2 = 3.6.
Cheers,
Erik
Baofu Qiao skrev 2011-05-17 15.57:
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.
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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