Closed xyko15 closed 6 years ago
The CG structure is linear in the sense that it's only connected by bonds 1->2->3->4. The equilibrium bending angles are indeed not 0, suggested by the atomistic conformation. The bonded interactions might need to be slightly corrected (as noted in the paper) but overall I think it's doing the correct thing here. Alkanes don't form a straight line.
Thank you for checking this for me!
On Wed, Sep 5, 2018 at 2:16 AM Tristan Bereau notifications@github.com wrote:
The CG structure is linear in the sense that it's only connected by bonds 1->2->3->4. The equilibrium bending angles are indeed not 0, suggested by the atomistic conformation. The bonded interactions might need to be slightly corrected (as noted in the paper) but overall I think it's doing the correct thing here. Alkanes don't form a straight line.
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I am trying to use auto_martini to coarse grain a small surfactant molecule(quaternary ammonium), and I break the molecule into head and tail parts. When I use auto martini to generate the structure for the tail, I got the following output. This coarse-grained tail is not linear, which does not appear correct to me.
I did use python 2to3 to change the code so that I can use it with python 3, but other than that, it works ok. I just want to check whether my code has problems or this will be the structure auto_martini code is gonna generate.
(my-rdkit-env) C:\martini>python auto_martini --smi "CCCCCCCCCCCCCCCC" --mol Quattail --gro quattail.gro ;;;; GENERATED WITH auto-martini ; INPUT SMILES: CCCCCCCCCCCCCCCC ; Tristan Bereau (2014)
[moleculetype] ; molname nrexcl Quattail 2
[atoms] ; id type resnr residu atom cgnr charge smiles 1 C1 1 Quattail C01 1 0 ; CCCCC 2 C3 1 Quattail C02 2 0 ; CCC 3 C3 1 Quattail C03 3 0 ; CCC 4 C1 1 Quattail C04 4 0 ; CCCCC
[bonds] ; i j funct length force.c. 1 2 1 0.31 1250 2 3 1 0.35 1250 3 4 1 0.32 1250
[angles] ; i j k funct angle force.c. 1 2 3 2 99.3 25.0 2 3 4 2 94.5 25.0