Re: [gmx-users] trjconv precision lost from double to single conversion
On Fri, Dec 12, 2014 at 4:31 PM, Johnny Lu wrote: > > Hi. I'm using gromacs 4.6.7 > > If the trr trajectory file is from double precision calculation, and I use > single precision trjconv to make a single precision trr trajectory, how > much precision will I lose in position and in force? > You'll go from practically infinite precision for any such quantity to about 6 significant figures, ie. double floating-point precision to single. Their representations are kind of like scientific notation. Read up on wikipedia about those :-) 1, 0.1, 0.01, or 0.001 angstrom and Newton? > That depends on the magnitude of the numbers. You're getting a change in relative precision. Is the lost of precision acceptable? > Depends what you're using them for. > I noticed that single precision trr seems to take about half the hard disk > space of double precision trr. > Yep. Mark > > Thank you. > -- > 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] trjconv precision lost from double to single conversion
nevermind the 2nd question. it does reduce to about 1/10 size. On Fri, Dec 12, 2014 at 10:41 AM, Johnny Lu wrote: > > When I test the disk space that I would save by getting rid the water in > the trajectory, I found that only make the trajectory 1/4 as large as the > original. > The trajectory has both position and force. > > Yet, the proteins only have about 1/10 the number of atoms of the whole > system. > > Group 0 ( System) has 29859 elements > Group 1 (Protein) has 2598 elements > > Should the trajectory file size reduced to 1/4 instead of 1/10? > > The command that I used was: > echo -e "1\n1\n" | $GMXHOME/trjconv_d -f $In_Traj -o $Out_Traj -s $In_ptr > -pbc mol -ur compact -center -force > > Thanks again. > > On Fri, Dec 12, 2014 at 10:31 AM, Johnny Lu > wrote: >> >> Hi. I'm using gromacs 4.6.7 >> >> If the trr trajectory file is from double precision calculation, and I >> use single precision trjconv to make a single precision trr trajectory, how >> much precision will I lose in position and in force? >> >> 1, 0.1, 0.01, or 0.001 angstrom and Newton? >> >> Is the lost of precision acceptable? >> >> I noticed that single precision trr seems to take about half the hard >> disk space of double precision trr. >> >> Thank you. >> > -- 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] trjconv precision lost from double to single conversion
When I test the disk space that I would save by getting rid the water in the trajectory, I found that only make the trajectory 1/4 as large as the original. The trajectory has both position and force. Yet, the proteins only have about 1/10 the number of atoms of the whole system. Group 0 ( System) has 29859 elements Group 1 (Protein) has 2598 elements Should the trajectory file size reduced to 1/4 instead of 1/10? The command that I used was: echo -e "1\n1\n" | $GMXHOME/trjconv_d -f $In_Traj -o $Out_Traj -s $In_ptr -pbc mol -ur compact -center -force Thanks again. On Fri, Dec 12, 2014 at 10:31 AM, Johnny Lu wrote: > > Hi. I'm using gromacs 4.6.7 > > If the trr trajectory file is from double precision calculation, and I use > single precision trjconv to make a single precision trr trajectory, how > much precision will I lose in position and in force? > > 1, 0.1, 0.01, or 0.001 angstrom and Newton? > > Is the lost of precision acceptable? > > I noticed that single precision trr seems to take about half the hard disk > space of double precision trr. > > Thank you. > -- 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] trjconv precision lost from double to single conversion
Hi. I'm using gromacs 4.6.7 If the trr trajectory file is from double precision calculation, and I use single precision trjconv to make a single precision trr trajectory, how much precision will I lose in position and in force? 1, 0.1, 0.01, or 0.001 angstrom and Newton? Is the lost of precision acceptable? I noticed that single precision trr seems to take about half the hard disk space of double precision trr. Thank you. -- 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.
