[gmx-users] RMSD Matrix error

[Mark Abraham]

Hi,

On Sun, Jun 4, 2017 at 4:08 PM Apramita Chand <apramita.chand at gmail.com>
wrote:

> Dear All,
>
> When I'm trying to construct a RMSD matrix , using the command
> g_rms  -s protein_equili.gro   -f  protein_model1_ut.xtc   -m
> rmsd-matrix.xpm  -tu ns
>
> I get the error:
> Last frame     200000 time   20.000
>
> Building RMSD matrix, 200001x200001 elements
>  element 28982; time  2.90  Killed
>

That matrix has 4x10^10 elements, each of which needs 4 bytes of memory.
1GB is about 1x10^9 bytes, so you'd need at least 160 GB of memory.

The real issue is that you are probably using a large number of highly
correlated frames, so even if you could form the full distance matrix, you
would not learn any more than you would from a matrix formed from a
suitable sub-sampling.


> I have given the reference structure to be the one prior to production run
> and after equilibration step. I have also tried the command with .tpr file.
> Same error!
>

The problem doesn't change with the nature of the reference structure.

Mark


> How to solve this?
>
>
> yours sincerely
> Apramita
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