Dear Wesley and Karolina,
Thank you both for your exciting advice.
Wesley, for such a well-explained solution. Thank you for your efforts.
And Karolina, I will surely test Aquaduct and would love to give my
feedback. This tool might help me in other projects too. Thank you for the
many ideas.
Best regards,
Chetna Tyagi
On Wed, Jun 12, 2019 at 10:40 PM Karolina Mitusińska (Markowska) <
markowska.kar.gmail.com> wrote:
> 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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--
Best wishes
Chetna
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Received on Thu Jun 13 2019 - 02:00:02 PDT
