Re: [AMBER] Regarding nmode error

From: Rajarshi Roy <>
Date: Mon, 1 Jul 2019 19:19:01 +0530

Dear Sir,

Sorry for the ambiguity. I want to say that after a certain number of
iteration. I have a 410 residue long protein- RNA complex. I am running my
calculation in centos environment having 32 GB RAM. I used 25 frames only
for my calculations, but still, I am getting the same error.

On Mon, Jul 1, 2019 at 6:28 PM David A Case <> wrote:

> 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.
> ....dac
> _______________________________________________
> AMBER mailing list

*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
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Received on Mon Jul 01 2019 - 07:00:02 PDT
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