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本帖最后由 Frozen-Penguin 于 2022-8-4 22:37 编辑
结构不仅取决于键长键角二面角，也与非键相互作用有关，键长键角一般是不变的，但是二面角比较弱，是可以变化的，最低能构象中的二面角能量不一定是最低的，同时考虑非键相互作用能量才是最低的，所以如果加大二面角的力常数，让二面角处于能量最低状态，反而可能会让结构偏离低能构象，所以如果要约束二面角应该用dihedral restraint，给二面角加上简谐势，https://manual.gromacs.org/curre ... dihedral-restraints
plumed:
- rmsd: RMSD ... # calculate RMSD
- REFERENCE=ref.pdb # the reference structure which only contains the atoms you want to calculate
- TYPE=OPTIMAL # remove COM transformation and rotation before calculation
- ...
- # How to get the reference PDB ?
- # The reference PDB should contains the index and positions of atoms,
- # and the index should be the same as what gromacs reads in.
- # gmx editconf -f md.tpr -o tmp.pdb
- # Usually we only calculate with C-alpha.
- # grep CA tmp.pdb > ref.pdb
- # Then delete the atoms we do not want to use.
- restraint: RESTRAINT ... # restraint
- ARG=rmsd # restraint was applied to RMSD
- KAPPA=10.0 # the strength of restraint, try different values to find a good one
- AT=0.0 # prevent RMSD from rising
- ...
- # write the values of RMSD and the bias every 500 steps
- PRINT ARG=rmsd,restraint.bias FILE=log.txt STRIDE=500
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发表于 Post on 2022-7-21 18:04:48
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发表于 Post on 2022-7-21 18:33:39
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