[gmx-users] Fundamental Units of MDS Package (time unit t = 48.88821 femtoseconds)
Hello there, I am writing to seek clarification regarding the fundamental units of a molecular dynamics package. In the manual it clearly states that the fundamental units are as follows: Length Angstrom (0.1nm); Energy kcal/mol; Temperature Kelvin and Mass g/mol. Further these yield the derived units: - time unit t = 48.88821 femtoseconds I used a separate code for the simulation and am employing GROMACS version 5.1.2 to perform trajectory analysis. However, I am somewhat confused by the time unit of 48.88821 fs. I ran a microsecond-long simulation (~1000 ns) and the system (under investigation) equilibrated at 250 ns. However the output files (most notably the .xvg files) would suggest that the system equilibrated at 2.50e+08 picoseconds (= 25 nanoseconds). If, however the figure above (2.50e+08) was expressed in femtoseconds, then there would be no confusion. I would be most grateful for any comments you may wish to make regarding this matter. Thank you in advance. Sent with [ProtonMail](https://protonmail.com) Secure Email. -- 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] Carbon-Alpha RMSD Plots
Hello there, I am writing to seek clarification regarding the following: I use GROMACS version 5.1.2 and Grace (xmgrace) version 5.1.25 I ran a molecular dynamics simulation for 1 microsecond (~ 1055 ns). I used xmgrace to plot a carbon-alpha RMSD plot and I noticed that the x-axis [Time (picoseconds)] is suggestive of the fact that the total simulation time was 1e+09 picoseconds (1000 microseconds). Furthermore, invocation of gmx rms did not involve the option -tu, therefore it was set to default (i.e., picoseconds). I discarded the initial portion to equilibration (250 ns). The question I have is if I considered the values in femtoseconds then the RMSD plot as it appears makes absolute sense, however the x-axis is clearly set in picoseconds. I thank you for your kind assistance. Yours faithfully, JT Sent with [ProtonMail](https://protonmail.com) Secure Email. -- 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 check precision
Hello there, I am currently using GROMACS version 5.1.2 and had a question in relation to the gmx check command. The following appears on the screen after invocation of gmx check -f protein.pdb: GROMACS: gmx check, VERSION 5.1.2 Executable: /usr/bin/gmx Data prefix: /usr Command line: gmx check -f protein.pdb Checking file protein.pdb Reading frame 0 time0.000 # Atoms 9190 Precision 0.0001 (nm) 'GROtesk MACabre and Sinister t= 40.0', 9190 atoms Reading frame6000 time 24.000 Item#frames Timestep (ps) Step 625040 Time 625040 Lambda 0 Coords625040 Velocities 0 Forces 0 Box 0 The precision = 0.001 nm, all my attempts at locating the answer for my questions proved futile. Question) Invocation of similar command for XTC file (i.e., gmx check -f protein.xtc) also results in precision of 0.001 nm. However, in the manual it clearly states that .xtc exhibits greater precision in comparison to .pdb. If that is the case, then why am I observing the same value for precision in both? Or is it the case that because the system under investigation only contains 9,190 atoms, therefore the difference in precision between .xtc and .pdb is almost negligible and only realised when a much larger system is under investigation? FInally, could you kindly summarise the significance of precision obtained from gmx check command for a beginner? I thank you in advance for your kind assistance. Yours faithfully, J. Sent with [ProtonMail](https://protonmail.com) Secure Email. -- 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.
