Hi,
In packmol-memgen you should be able to stack membranes by callin --lipids more than once. Check the manual for that. For Charmm-GUI, you'd have to check their webpage.
Best regards,
Thompson, Emma via AMBER <amber.ambermd.org<mailto:
amber.ambermd.org>> schrieb am Di., 20. Feb. 2024, 17:06:
Hello,
I would like to establish a concentration gradient across a bilayer to look at ions going through a protein channel. I have created a starting gradient, but it is dissipating due to the periodic boundary conditions. One way others have gotten around this is to stack membranes:
"Stack oriented along the z axis, the water at each end is contiguous, due to the periodic boundary conditions. A much larger system would be needed, as a vertical stack of
water
bilayer
water
water
bilayer
water
which isolates the central water layer from those at the -z and +z ends of the simulation cell."
Does anyone know if this is possible to do with Charmm's membrane builder to then simulate in Amber, and if so, how to do so?
Thanks,
Emma
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Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
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Received on Tue Feb 20 2024 - 13:30:03 PST
