Re: [gmx-users] rdf at contact
I will be grateful if some one can reply my question, Best regards On Wed, May 30, 2018 at 4:45 PM, Faezeh Pousaneh wrote: > Hi, > > I have a system of similar molecules, I would like to obtain the rdf at > contact (meaning, at surface of one particle). > What I try is; I make an index file containing only central atoms of all > molecules, then I run: > > > gmx rdf -f NPT.xtc -s NPT.tpr -n index.ndx -pbc -ref 1 -sel 0 > -b 14000 > > ref 0 is a single atom > ref 1 is rest of atoms > > > Then, I find the rdf value at r=contact (radius of a molecule) from > rdf.xvg file. > My problem is I get very different values for different time intervals > (after equilibrium) . Why is that so? > > I appreciate if sb can help. > Best regards > > -- 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.
Re: [gmx-users] rdf at contact
How noisy is the rdf i.e. what is the bin width, how many atoms etc? Have you graphed the entire function? That would be my first suggestion of the cause. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On 31 May 2018 at 00:45, Faezeh Pousaneh wrote: > Hi, > > I have a system of similar molecules, I would like to obtain the rdf at > contact (meaning, at surface of one particle). > What I try is; I make an index file containing only central atoms of all > molecules, then I run: > > > gmx rdf -f NPT.xtc -s NPT.tpr -n index.ndx -pbc -ref 1 -sel 0 -b > 14000 > > ref 0 is a single atom > ref 1 is rest of atoms > > > Then, I find the rdf value at r=contact (radius of a molecule) from rdf.xvg > file. > My problem is I get very different values for different time intervals > (after equilibrium) . Why is that so? > > I appreciate if sb can help. > Best regards > -- > 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. -- 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] rdf at contact
Hi, I have a system of similar molecules, I would like to obtain the rdf at contact (meaning, at surface of one particle). What I try is; I make an index file containing only central atoms of all molecules, then I run: gmx rdf -f NPT.xtc -s NPT.tpr -n index.ndx -pbc -ref 1 -sel 0 -b 14000 ref 0 is a single atom ref 1 is rest of atoms Then, I find the rdf value at r=contact (radius of a molecule) from rdf.xvg file. My problem is I get very different values for different time intervals (after equilibrium) . Why is that so? I appreciate if sb can help. Best regards -- 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.
