[gmx-users] Umbrella sampling simulations using make_edi with -restrain and -harmonic
ckutzne at gwdg.de
Tue Sep 10 10:21:32 CEST 2013
On Sep 10, 2013, at 9:53 AM, "Chen, Po-chia" <pchen at gwdg.de> wrote:
> 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
I think you should add -tau 0 when using flooding as harmonic restraint
(since you do not want the flooding potential to change).
> 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.
Can you check whether make_edi -ori wrote the correct position on the 1st eigenvector in your
.edi file? Scroll down to a line called
# NUMBER OF EIGENVECTORS + COMPONENTS GROUP 7
(Group 7 means the flooding vectors), if you have a single flooding vector, the next
line should read "1" and in the following line you will find three entries that describe
<nr> <spring constant> <reference projection> <ref. proj. change per time step>
which I guess read in your case
1 1 9.99 <no 4th entry>
so the reference projection should be 9.99, as calculated from your .ori structure.
If there is no 3rd entry, you can simply put it there manually (and leave away
the -ori option to make_edi).
> = = =
> P.S. the relevant constrain.edi lines contain:
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
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