Hi there,
I recommend the AQUA-DUCT software, the product of my research group.
This is a software that tracks water molecules (but not only, small
ligands, too!) during MD simulations. We haven't test it on membranes yet,
so if you would like to try please do not hesitate to visit our website:
http://www.aquaduct.pl/ and contact us for some support.
We are also working on a new release with more advanced options, so we'd
appreciate all feedback :)
Best regards,
Karolina Mitusińska
PhD student
śr., 12 cze 2019 o 18:28 Chetna Tyagi <cheta231.gmail.com> napisał(a):
> Dear Amber users,
>
> I would like to calculate the number of water molecules that crossed
> through the pore as a function of simulation time from one end to another.
>
> The hexameric pore is set in a DOPC:DOPG bilayer membrane. I have tried
> 'diffusion' calculation but it doesn't calculate the number of water
> molecules passing through the pore.
>
> Any ideas will help me a lot. Thanks.
>
> --
> Best wishes
> Chetna
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Received on Wed Jun 12 2019 - 14:00:03 PDT
