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Commit 6e34c347 authored by Massimiliano Bonomi's avatar Massimiliano Bonomi
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more details for tutorial 6

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......@@ -59,14 +59,54 @@ The users are free to choose his/her favorite CVs and they are encouraged to use
on-line manual to create their own PLUMED input file.
However, we encourage all the users to experiment at least with the following CVs:
1) \ref RMSD and/or \ref DRMSD from the native state (provided in `bard1_native.pdb`)
1) \ref RMSD and/or \ref DRMSD from the native state
2) Number of inter-chains contacts (specific, i.e. native, or all)
This can be achieved with either \ref COORDINATION or \ref CONTACTMAP.
The following line can be added to the `plumed.dat` file to calculate the \ref RMSD on the beads
representing the backbone aminoacids:
\plumedfile
rmsd: RMSD REFERENCE=bard1_rmsd.pdb TYPE=OPTIMAL
\endplumedfile
while this one can be used to calculate the \ref DRMSD between chains:
\plumedfile
drmsd: DRMSD REFERENCE=bard1_drmsd.pdb TYPE=INTER-DRMSD LOWER_CUTOFF=0.1 UPPER_CUTOFF=1.5
\endplumedfile
2) Number of inter-chains contacts (specific, i.e. native, or all).
This can be achieved with the \ref COORDINATION CVs, as follows:
\plumedfile
# backbone beads index for chain A
chainA: GROUP ATOMS=1,3,5,7,9,10,12,15,17,19,21,23,25,27,29,31,33,34,36,38,41,43,45,47,49,51,53,55,57,59,61,63,66,68,70,72,74,76,79,81,83,87,89,93,95,98,102,104,106,108,111,113,115,117,119,122,125,126,128,130,132,134,136,138,140,143,145,147,149,151,154,157,159,161,163,165,167,169,172,176,178,180,182,184,186,188,190,192,195,197,199,201,202,206,208,210,212,214,215,217,219,223,224
# backbone beads index for chain B
chainB: GROUP ATOMS=226,228,230,232,234,235,238,239,240,245,246,250,252,255,256,257,259,261,264,266,268,271,273,275,278,280,282,285,287,289,291,293,295,298,300,302,304,306,308,309,310,312,314,318,320,324,326,328,330,332,334,336,338,340,342,343,345,346,348,350,352,354,358,360,362,363,368,370,372,374,376,379,381,383,386,388,390,392,394,396,398,400,402,404,406,409,411,414,416,418,420,424,426,428,430,432,434
coord: COORDINATION GROUPA=chainA GROUPB=chainB NOPBC D_0=1.0
\endplumedfile
3) A CV describing the relative orientation of the two chains.
This can be achieved, for example, by defining suitable virtual atoms with the \ref CENTER
keyword and the \ref TORSION CV.
keyword and the \ref TORSION CV:
\plumedfile
# virtual atom representing the first half of chain A
chainA_1: CENTER ATOMS=__FILL__
# virtual atom representing the second half of chain A
chainA_2: CENTER ATOMS=__FILL__
# virtual atom representing the first half of chain B
chainB_1: CENTER ATOMS=__FILL__
# virtual atom representing the second half of chain B
chainB_2: CENTER ATOMS=__FILL__
# torsion CV
dih: TORSION ATOMS=__FILL__
\endplumedfile
\section trieste-6-ex-2 Exercize 2: analysis of the cmyc-urea simulation
......
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