Re: [gmx-users] regarding hydrogen bond correlation function for Cdd for TIP4P/2005 water model
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.markl...@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.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> > > On 13 Sep 2017, at 06:16, Abhinav Srivastava (P14CHM002) < > srivastav...@iitj.ac.in<mailto:srivastav...@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 > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org<mailto:gmx-users-request@ > gromacs.org>. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- *Abhinav Srivastava* *Research Scholar* Indian Institute of Technology, Jodhpur Rajasthan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] regarding hydrogen bond correlation function for Cdd for TIP4P/2005 water model
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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] regarding
Dear Gromacs Users, 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] regarding posting queries in gromacs mailing list
Dear Gromacs developers, Following is my email address for posting queries to GROMACS srivastav...@iitj.ac.in Best regards, *Abhinav Srivastava* *Research Scholar* Indian Institute of Technology, Jodhpur Rajasthan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
