Re: [AMBER] Regarding nmode error

From: David A Case <>
Date: Mon, 1 Jul 2019 08:57:14 -0400

On Sun, Jun 30, 2019, Rajarshi Roy wrote:
>I am trying to calculate the entropy of an RNA-protein complex using nmode.
>But I am getting following error.
>FATAL: allocation failure in vector()

This means the system cannot allocate enough memory for your problem.

>The same trajectory and topology, I used in my previous MMPBSA analysis. I
>also try this nmode analysis with lesser number frame, but I get the same
>error after certain number of steps. I am not able to understand the reason
>of such error.

What do you mean by "after a certain number of steps"? (Steps of what?)
It could be that other jobs are using memory on your computer system, so
that the amount of memory available to you might change from time to
time. You could also see if changing the number of MPI threads has an
impact on the result.


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Received on Mon Jul 01 2019 - 06:00:03 PDT
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