Dear GMX-users
I have a question about what happens when editconf is used to "box" a molecule. The reason I ask is because, I have used g_rmsdist in order to study how a very small piece of a structure (100+ atoms) relaxes towards its native state (given by NMR) after a small perturbation. After 10+ ns the distrmsd has not been below 0.25 nm. Tracing back, I realized that the distrmsd was already 0.25 nm after I inserted my NMR structure into the box in the first place! I did the following: 1. editconf -f NMR.gro -o boxed.gro -box 4 4 4 2. /apps/gromacs4/bin/g_rmsdist -f boxed.gro -s NMR.gro -o distrmsd-boxed-NMR .. Select a group: 0 Selected 0: 'System' .. 3. cat distrmsd-boxed-NMR.xvg # This file was created Fri Sep 18 13:02:06 2009 # by the following command: # /apps/gromacs4/bin/g_rmsdist -f boxed.gro -s NMR.gro -o distrmsd-boxed-NMR # # /apps/gromacs4/bin/g_rmsdist is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @ title "RMS Deviation" @ xaxis label "Time (ps)" @ yaxis label "RMSD (nm)" @TYPE xy @ subtitle "of distances between System atoms" 0 0.249025 Just as a test, I tried also *NOT* to box the structure: 1. editconf -f NMR.gro -o test.gro 2. /apps/gromacs4/bin/g_rmsdist -f test.gro -s NMR.gro -o distrmsd-boxed-NMR ... Select a group: 0 Selected 0: 'System' ... 3. cat distrmsd-boxed-NMR.xvg # This file was created Fri Sep 18 13:16:04 2009 # by the following command: # /apps/gromacs4/bin/g_rmsdist -f test.gro -s NMR.gro -o distrmsd-boxed-NMR # # /apps/gromacs4/bin/g_rmsdist is part of G R O M A C S: # # Giant Rising Ordinary Mutants for A Clerical Setup # @ title "RMS Deviation" @ xaxis label "Time (ps)" @ yaxis label "RMSD (nm)" @TYPE xy @ subtitle "of distances between System atoms" 0 1.83827e-08 Why I am seeing this difference? Is it due to round-off's after the transformation to center the molecule in the box? Or am I using g_rmsdist wrongly? Best regards, Soren
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