[gmx-users] Umbrella sampling simulations using make_edi with -restrain and -harmonic
pchen at gwdg.de
Tue Sep 10 09:53:40 CEST 2013
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 \
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:
More information about the gromacs.org_gmx-users