I think you should add -tau 0 when using flooding as harmonic restraint
(since you do not want the flooding potential to change).
Okay, adding -tau 0 does turn it properly into a harmonic potential,
according to edsam.xvg. However, the average position of the resulting
(gaussian) is near but not at the expected value, given the reference
position in -ori.
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).
constrain.edi with the -tau 0 line and -ori does not give the reference
position on the eigenvector. -ori seems to only write the new origin
coordinates. So the output looks like this:
...
# NUMBER OF EIGENVECTORS + COMPONENTS GROUP 7
1
1 0.052626 #<-- lack of reference position after vector and
spring-constant.
-0.04593 -0.02711 -0.01672
-0.04696 -0.01819 -0.00113
...
#NTARGET, XTARGET
0
#NORIGIN, XORIGIN
574
7 8.208000 9.368000 4.211000 #<-- coordinates change with -ori argument
...
I'll put the values in manually and run another set.
- Po-chia.
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