[gmx-users] regarding hydrogen bond correlation function for Cdd for TIP4P/2005 water model

Erik Marklund erik.marklund at kemi.uu.se
Wed Sep 13 12:00:16 CEST 2017

Dear Abhinav,

This is a bit tricky. We implemented the geminate recombination model some time ago, but have taken it our of the gmx hbond tool because it complicates the code quite a lot.

That said, if you want to use that old code you first need to "pbc-unwrap” your trajectory using trjconv -nojump. Try that and see if you get more reasonable output.

Kind regards,
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 13 Sep 2017, at 06:16, Abhinav Srivastava (P14CHM002) <srivastava.2 at iitj.ac.in<mailto:srivastava.2 at iitj.ac.in>> wrote:

Dear Gromacs Users,

Kindly consider this as my query mail as in the last mail, subject line was
not complete. I apologize for the same .
I am trying to calculate hydrogen bond correlation function Cdd(t) for bulk
water (TIP4P/2005 water) using reversible geminate recombination as
mentioned in
Markovitch et al., J. Chem. Phys.,129,084505(2008).

Following is the command which I have used :

g_hbond -f NVT.xtc -s NVT.tpr -n bulk-water.ndx -b 0 -e 100 -P 1 -temp 308
-geminate dd -ac Cdd-bulk-water.xvg

I have simulated two systems viz. smaller system consisting of 851 water
molecules and a bigger system consisting of 1944 water molecules. I am not
able to get t^-3/2 scaling in hydrogen bond correlation function for Cdd
case in both these systems. It would be nice if you can please help me.
Thanks in advance.

*Abhinav Srivastava*
*Research Scholar*
Indian Institute of Technology, Jodhpur
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