Re: [gmx-users] gmx trjconv trr xtc
Hi, XTC is a reduced-precision format for coordinates. This is fine for most use cases, because the difference between 2.012 nm and 2.013nm is dwarfed by the other modelling approximations (fixed point charges! short sampling!). It gives you the advantage of using less disk and spending less time handling files. Further, it leverages the knowledge that in e.g. a water molecule, the three atoms are not in arbitrary locations, but can be stored efficiently as a position and two deltas. See http://manual.gromacs.org/documentation/current/reference-manual/file-formats.html#xtc Mark On Tue, 12 Mar 2019 at 00:57 Alex wrote: > Dear groamcs user, > A system of mine contains two molecule type of A and B in water. Using > gmx trjconv -f out.xtc -o out.last.5ns.trr I first truncated the last 5ns > of the system's XTC file as a TRR file and just selected the non-water > contents so that the TRR file only has A and B. The TRR file is 4.4 GB. > Then I applied again the "gmx trjconv -pbc cluster -center yes -f > out.last.5ns.trr -o out.last.5ns.xtc" and again just non-water was chosen. > I was expecting that the both out.last.5ns.trr and out.last.5ns.xtc would > have the same size 4.4 GB as the material in both of them are just A and B, > however, the out.last.5ns.xtc is just 1.4 GB! > I wonder if that is normal? here I just care about the coordinates > dynamically and not velocity, do you think I am loosing any coordinate in > by the second command from out.last.5ns.trr to out.last.5ns.xtc? > > Regards > Alex > -- > 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] gmx trjconv trr xtc
.trr and .xtc are two different file formats, with the latter being compressed. Therefore, an .xtc file will be significantly smaller than a .trr 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 Tue, 12 Mar 2019 at 10:56, Alex wrote: > Dear groamcs user, > A system of mine contains two molecule type of A and B in water. Using > gmx trjconv -f out.xtc -o out.last.5ns.trr I first truncated the last 5ns > of the system's XTC file as a TRR file and just selected the non-water > contents so that the TRR file only has A and B. The TRR file is 4.4 GB. > Then I applied again the "gmx trjconv -pbc cluster -center yes -f > out.last.5ns.trr -o out.last.5ns.xtc" and again just non-water was chosen. > I was expecting that the both out.last.5ns.trr and out.last.5ns.xtc would > have the same size 4.4 GB as the material in both of them are just A and B, > however, the out.last.5ns.xtc is just 1.4 GB! > I wonder if that is normal? here I just care about the coordinates > dynamically and not velocity, do you think I am loosing any coordinate in > by the second command from out.last.5ns.trr to out.last.5ns.xtc? > > Regards > Alex > -- > 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] gmx trjconv trr xtc
Dear groamcs user, A system of mine contains two molecule type of A and B in water. Using gmx trjconv -f out.xtc -o out.last.5ns.trr I first truncated the last 5ns of the system's XTC file as a TRR file and just selected the non-water contents so that the TRR file only has A and B. The TRR file is 4.4 GB. Then I applied again the "gmx trjconv -pbc cluster -center yes -f out.last.5ns.trr -o out.last.5ns.xtc" and again just non-water was chosen. I was expecting that the both out.last.5ns.trr and out.last.5ns.xtc would have the same size 4.4 GB as the material in both of them are just A and B, however, the out.last.5ns.xtc is just 1.4 GB! I wonder if that is normal? here I just care about the coordinates dynamically and not velocity, do you think I am loosing any coordinate in by the second command from out.last.5ns.trr to out.last.5ns.xtc? Regards Alex -- 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.
