AMBER Archive (2008)

Subject: AMBER: nmode/nab entropy calculations without hydrogens

From: chaitanya koppisetty (ashok_at_chalmers.se)
Date: Wed Sep 17 2008 - 02:47:58 CDT

Thanks for the comments.

I am still thinking if it would be reasonable to do the calculations by
stripping of the hydrogens.(This reduced the atom count so that there are
no memory issues) I am not sure if the results would be meaningful. The
aim of the entropy calculations is to use it for binding energy
calculations for a protein-protein and for a protein-ligand system.

Regards,
Chaitanya.

> Hi,
>> I have a question relating to entropy calculations using nmode/nab. I am
>> trying to calculate entropy of a protein which has around 9000 atoms. I
>> encountered memory problems both with nmode and nab.
>
>> Any estimate of how much memory I might need to run this kind of system
>> ?
> Your system contains 27000 coordinates, which makes 27000**2 = 729 million
> entries, each of which needs 8 bytes, which gives 5.8 billion bytes for
> the hessian (though the hessian is symmetric and exploiting this can save
> memory - I'm not sure about implementation details).
>
> Anyway: For 6370 atoms, I see 5.9 GB of memory being used (so this
> woudln't work within reasonable time on a 4GB machine).
> For 9515 atoms I see 13 GB of memory in use. So you might like a 16 GB
> machine for this (at least).
>
> ...good luck
> Andreas
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