[gmx-users] Protein pore collapse during simulation.

[Justin Lemkul]

On 2/1/20 5:05 AM, Yogesh Sharma wrote:
> sir,
>   in efforts to find out the differences in the density of bilayers
> generated by charmm and gromac(berger lipids) i used grid-mat. there are
> significant differences in area per lipid.
>
> with these settings for both systems:
> override_vectors        5.2,10.0,6.9
> grid                    20
> conserve_ratio          yes
> protein                 yes
> precision               1.3
> P_value                 5.0
> #Lower Z limit: 3.036   Upper Z limit: 7.784
>
> charmm with hydrogen (sq. A)
> area per lipid upper leaflet: 10.5
> area per lipid bottom leaflet 5.45
>
> charmm (bilayer saved without hydrogen) (sq. A)
> area per lipid upper leaflet: 13
> area per lipid bottom leaflet 7

This looks like something is wrong with the way you've calculated the 
areas, but without access to your input files there's nothing more I can 
say.

-Justin

> gromac (sq. A)
> area per lipid upper leaflet: 70
> area per lipid bottom leaflet 68
> Are charmm values below experimental observation for POPC i.e gelation of
> bilayer?

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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