Re: [gmx-users] Print Neighbour list
Thank you for your answer. Unfortunately, that is exactly what I am trying to do. However, what I need is more of a custom neighbour search for specific particle-water interactions (i.e. one atom against all the neighbour water molecules), than a completely new class. And I need to do it at runtime, since I will use this information as input for other operations. However, I think I got the gist of it, thanks to your previous answer. Again, thanks for everything. Best, Paolo Il 28/01/2019 14:03, Mark Abraham ha scritto: Hi, gmx select does this kind of operation already, if what you want to do is not part of the simulation... It is implemented by its own simple but fairly efficient search. The neighbor search code is intended for consumption by the short-range kernels, and you do not want to get involved with that unless you have to! Mark On Mon, 28 Jan 2019 at 12:49 Paolo Conflitti wrote: Thanks for your prompt reply. I wanted to print the neighbour list to better understand the way it is processed. I am currently trying to modify the Gromacs code in order to print only the neighbour list of the water molecules around a certain atom. I got inside the code and I found the algorithms that process this kind of information, but I also wanted to see how the data are organized. May I ask you if you know of a different way or variable (maybe a commented line somewhere inside Gromacs) that will allow me to do something similar? Best, Paolo -- 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.
Re: [gmx-users] Print Neighbour list
Hi, gmx select does this kind of operation already, if what you want to do is not part of the simulation... It is implemented by its own simple but fairly efficient search. The neighbor search code is intended for consumption by the short-range kernels, and you do not want to get involved with that unless you have to! Mark On Mon, 28 Jan 2019 at 12:49 Paolo Conflitti wrote: > Thanks for your prompt reply. > > I wanted to print the neighbour list to better understand the way it is > processed. > I am currently trying to modify the Gromacs code in order to print only > the neighbour list of the water molecules around a certain atom. I got > inside the code and I found the algorithms that process this kind of > information, but I also wanted to see how the data are organized. > May I ask you if you know of a different way or variable (maybe a > commented line somewhere inside Gromacs) that will allow me to do > something similar? > > Best, > Paolo > > -- > 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.
Re: [gmx-users] Print Neighbour list
Thanks for your prompt reply. I wanted to print the neighbour list to better understand the way it is processed. I am currently trying to modify the Gromacs code in order to print only the neighbour list of the water molecules around a certain atom. I got inside the code and I found the algorithms that process this kind of information, but I also wanted to see how the data are organized. May I ask you if you know of a different way or variable (maybe a commented line somewhere inside Gromacs) that will allow me to do something similar? Best, Paolo -- 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] Print Neighbour list
Hi, That's only supported by the group scheme, which is not the default in 2018.3. Probably the output would only be useful from a single-rank run, because the searching might be done and reported in terms of indices of atoms local to the domain being searched, rather than global. Mark On Mon, 28 Jan 2019 at 11:50 Paolo Conflitti wrote: > Dear Gromacs community, > > I am trying to print the neighbour list of my simulations. > Following the manual, I added the GMX_DUMP_NL environment variable in my > .profile bash file (export GMX_DUMP_LN=1). However, I cannot see any > neighbour list printed in my .log file. I am sure that the env variable > is properly read, since it appears inside the .log file. I am currently > using Gromacs 2018.3. > > Thank you in advance for any help you may give me. > > Best, > Paolo > > > -- > 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] Print Neighbour list
Dear Gromacs community, I am trying to print the neighbour list of my simulations. Following the manual, I added the GMX_DUMP_NL environment variable in my .profile bash file (export GMX_DUMP_LN=1). However, I cannot see any neighbour list printed in my .log file. I am sure that the env variable is properly read, since it appears inside the .log file. I am currently using Gromacs 2018.3. Thank you in advance for any help you may give me. Best, Paolo -- 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] Print neighbour list
Hi, In the code, it wants you to set GMX_DUMP_NL > 0. And please do everyone a favour and use a version of GROMACS that isn't over five years out of its supported lifetime :-) Mark On Sat, Feb 17, 2018 at 12:07 AM fabio trovato wrote: > Hi, > > I am trying to output the neighbor list calculated during a simulation. I > consulted the manual which says that DUMPNL is the env variable suited for > this purpose. > > In my bash script I first set up: > export DUMPNL=10 > > and then run the simulation (GROMACS version 4.5.4). > > I do not see any neighbor list printed in my md.log file. What am I doing > wrong? Does anyone knows how to solve this? > > Thank you, > Fabio > -- > 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] Print neighbour list
Hi, I am trying to output the neighbor list calculated during a simulation. I consulted the manual which says that DUMPNL is the env variable suited for this purpose. In my bash script I first set up: export DUMPNL=10 and then run the simulation (GROMACS version 4.5.4). I do not see any neighbor list printed in my md.log file. What am I doing wrong? Does anyone knows how to solve this? Thank you, Fabio -- 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.