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

[Abhinav Srivastava (P14CHM002)]

Dear Erik,

I tried unfolding the trajectory using trjconv -pbc nojump option as well.
But I did not get the correct t^-3/2 scaling. I am using Gromacs version
4.6.5.

Best regards,
Abhinav

On Wed, Sep 13, 2017 at 3:30 PM, Erik Marklund <erik.marklund at kemi.uu.se>
wrote:

> 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
> ______________________________________________
> 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
> Rajasthan
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-- 
*Abhinav Srivastava*
*Research Scholar*
Indian Institute of Technology, Jodhpur
Rajasthan