Re: MMPBSA calculation using CAFE plugin vmd

From: Pratik Narain Srivastava (
Date: Tue Sep 14 2021 - 07:03:41 CDT

There are a lot of technicalities here. First of all, do you really need to
calculate BFE for the entire 20 ns? I usually use the last frames of my
trajectory after checking that the simulation has converged sufficiently.
Or, as an alternative, you should put a stride of 10. You will sacrifice
some data but the global average BFE calculation should be fine.

On Tue, 14 Sep, 2021, 4:59 pm Nancy Singh, <> wrote:

> Hii,
> I did MMPBSA calculation using cafe plugin from VMD. I run the
> calculations for my 20ns trajectory file. Problem is it's taking a long
> time like almost 5 days for one calculation. Is there another way to make
> calculations faster? I run the calculation on NAMD 2.14 linux multicore.
> When I tried to run it with CUDA I got the error "Pair interaction
> calculation is not supported in CUDA version".
> Is there any way that I can run it on CUDA version? Any input on this will
> be really helpful.
> Thank you
> Regards,
> Nancy

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