[gmx-users] Protein pore collapse during simulation.

[Justin Lemkul]

On 1/18/20 7:03 AM, Yogesh Sharma wrote:
> Hi
> I have used inflategro to pack protein in lipid bilayer. While simulation
> run protein channel is getting collapsed. can i get some suggestions, if it
> is because of the wrong orientation of my protein in bilayer or lesser area
> per lipid after shrinking iterations? i have used charmm assembly as
> control, where protein channel is fine throughout trajectory. for
> inflategro packing i have used 128POPC fom calgiary university website.
>
> I reached an area of 0.67 nm2 while area in upper leaflet was 0.71 and in
> lowerleaflet it was 0.70nm2.
>
>    *thanks for your feedback and valuable time*

You've got many variables here. Are the number of lipids the same? The 
number of waters? Was each system equilibrated sufficiently to yield a 
stable state before the simulation started? The CHARMM-GUI methodology 
is far more robust than using InflateGRO and the C36 force field is much 
more accurate than the ancient Berger parameters.

-Justin

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Justin A. Lemkul, Ph.D.
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