Hi Po-chia,
On Sep 10, 2013, at 9:53 AM, Chen, Po-chia pc...@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
...
1.00 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 19.99 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).
Best,
Carsten
= = =
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
...
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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
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa
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