normal problem with PEO martini polymer forcefield

  • jmondal
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13 years 4 months ago #438 by jmondal
Hi,
I tried to use the Martini polymer forcefield for PEO for a system of single chain of PEO36 in water . But, I find the chain is getting extended in stead of collapsing to a gaussian chain( expected) as reported in the corresponding PEO paper. I was using PEO36.mdp, PEO36.gro and polymer itp files present in the Martini website . I am not sure what is going wrong. Any help to sort this problem will be appreciated.

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13 years 3 months ago #441 by xavier
Replied by xavier on topic problem with PEO martini polymer forcefield
Well it is not clear what can go wrong if you use the files on the website!

You might have modified something in the process of preparing your files!

You should try again from scratch.

XAvier.

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13 years 3 months ago #443 by siewert
Replied by siewert on topic problem with PEO martini polymer forcefield
Did you increase the self-interaction between the PEO beads?

See the following note which is taken from the martini_v2.0_polymers.itp file:

;
; Note: when using PEG or PEO, please make sure to change the following line in you
; martini_v2.x.itp file:
;
; SNa SNa 1 0.85338E01 0.53946E03 ; 75almost attractive, s=0.43
;
; (instead of
; SNa SNa 1 0.75856E01 0.47952E03 ; 75semi attractive, s=0.43)
;
; This is required to enhance the self-interaction between the PEO monomers
; to the level of an Nda particle,
;
; see Lee et al., J. Phys. Chem. B, 2009, 113 (40), pp 13186-13194 and
; Lee & Larson, J. Phys. Chem. B, 2009, 113 (40), pp 13202-13207
;
; Be cautious if you have other particles in your system of type 'SNa',
; their self-interaction will also be affected.
;

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