[gmx-users] regarding hydrogen bond correlation function for Cdd for TIP4P/2005 water model
erik.marklund at kemi.uu.se
Wed Sep 13 12:00:16 CEST 2017
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.
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
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.
Indian Institute of Technology, Jodhpur
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