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Martin Kurečka
Plumed AlphaFold
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0c0c0608
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Commit
0c0c0608
authored
5 years ago
by
Gareth Tribello
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Made changes to examples in Miscellaneous.md Please check these changes
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user-doc/Miscelaneous.md
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0c0c0608
...
...
@@ -23,7 +23,7 @@ erm... yes add lines of comments or trailing comments to your hearts content as
\p
lumedfile
# This is the distance between two atoms:
DISTANCE ATOM=1,2
LABEL=d1
d1:
DISTANCE ATOM
S
=1,2
UPPER_WALLS ARG=d1 AT=3.0 KAPPA=3.0 LABEL=Snout # In this same interlude it doth befall.
# That I, one Snout by name, present a wall.
\e
ndplumedfile
...
...
@@ -61,8 +61,7 @@ DISTANCES ...
Notice that the closing
`...`
is followed by the word
`DISTANCES`
. This is optional, but might be
useful to find more easily which is the matching start of the statement. The following is equally correct
\p
lumedfile
DISTANCES ...
LABEL=dist
dist: DISTANCES ...
# we can also insert comments here
ATOMS1=1,300
# multiple kewords per line are allowed
...
...
@@ -313,6 +312,8 @@ learn more.
In case you want to use this feature, we suggest you to put both label
and action type on the first line of multi-line statements. E.g.
\p
lumedfile
d: DISTANCE ATOMS=1,2
m: METAD ...
ARG=d
HEIGHT=1.0
...
...
@@ -322,10 +323,14 @@ m: METAD ...
\e
ndplumedfile
will be folded to
\v
erbatim
d: DISTANCE ATOMS=1,2
+-- 6 lines: m: METAD ...------------------------------------------------------
\e
ndverbatim
and
\p
lumedfile
d: DISTANCE ATOMS=1,2
METAD LABEL=m ...
ARG=d
HEIGHT=1.0
...
...
@@ -335,6 +340,8 @@ METAD LABEL=m ...
\e
ndplumedfile
will be folded to
\v
erbatim
d: DISTANCE ATOMS=1,2
+-- 6 lines: METAD LABEL=m ...-------------------------------------------------
\e
ndverbatim
This will allow you to easily identify the folded lines by seeing the most important information,
...
...
@@ -464,8 +471,8 @@ INCLUDE FILE=filename
So, for example, a single "plumed.dat" file:
\p
lumedfile
DISTANCE ATOMS=
0,1
LABEL=dist
RESTRAINT ARG=dist
DISTANCE ATOMS=
1,2
LABEL=dist
RESTRAINT ARG=dist
AT=2.0 KAPPA=1.0
\e
ndplumedfile
could be split up into two files as shown below:
...
...
@@ -487,7 +494,7 @@ is not possible to do things like:
\p
lumedfile
# this is wrong:
DISTANCE INCLUDE FILE=options.dat
RESTRAINT ARG=dist
RESTRAINT ARG=dist
AT=2.0 KAPPA=1.0
\e
ndplumedfile
\p
age load Loading shared libraries
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