Hi all, I can't seem to find the correct combination of EDI parameters impose a harmonically-constrained simulation along an eigenvector in GROMACS 4.6.2, and I'd like to confirm that the inputs I have are actually correct. Here is the make_edi command I used to generate the .edi file fed to mdrun:
echo "C-alpha System" | make_edi -restrain -harmonic \ -f ../ca-evec.trr \ -eig ../ca-eval.xvg \ -s ../analysis.tpr \ -ori ./init.gro \ -outfrq 2500 -deltaF0 150 -Eflnull 100 -flood 1 \ -o constrain.edi Where the eigenvectors and eigenvalues are previously derived by g_covar for a set of unrestrained trajectories. The origin file init.gro is the same as the starting coordinates of this constrained run, extracted from a previous EDI run to start at an appropriate location on the eigenvector space. The 1st eigenvalue is ~ 66, and the eigenvector looked fine in VMD when plotted by g_anaeig -extr. So mdrun -ei constrain.edi runs normally, but the flooding potential drops to zero so the protein diffuses freely along the 1st eigenvector. e.g. the first/last line in edsam.xvg looks like: # time RMSD EV1projFLOOD EV1-Ef1 EV1-Vf1 EV1-deltaF 0.0 0.43 9.99 -9.4e+1 9.5e-8 3.8e-9 -5.3e-4 10.0 0.40 9.49 0.0 -0.0 1.6e-44 -0.0 ... 10000.00 0.94 -2.2 0.0 -0.0 1.6e-44 -0.0 When c(0) is supposed to be according 9.99 as I set init.gro to be the -ori. Do I need to change -alpha as well? What parameters am I missing/added by mistake? The manual gives no indication as to which ones to do. = = = P.S. the relevant constrain.edi lines contain: ... #DELTA_F0 150.00 #INIT_DELTA_F 0.0 #TAU 0.10 #EFL_NULL -100.00 #ALPHA2 -1.0 #KT 2.50 #HARMONIC 1 #CONST_FORCE_FLOODING 0 ... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
