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tbereau / auto_martini

Automatic MARTINI parametrization of small organic molecules
GNU General Public License v2.0
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the structure generated does not look right #13

Closed xyko15 closed 6 years ago

xyko15 commented 6 years ago

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

tbereau commented 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.

xyko15 commented 6 years ago

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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