[gmx-users] RMSD Matrix Error

[Mark Abraham]

Hi,

You might want to measure the autocorrelation time of RMSD from your
reference structure. Then you'll have an idea how long you have to wait to
make a statistically independent observation.

Mark

On Tue, 6 Jun 2017 08:25 Apramita Chand <apramita.chand at gmail.com> wrote:

> Dear Mark,
> Thanks for your reply. I think you're right about the space needed for
> generating RMSD Matrix. I definitely was short of 160GB !!
> Further, you've talked about me using highly correlated frames and that a
> suitable sub-sampling might solve the problem. How would I know which
> frames to use?
>
>
>
> Message: 2
> Date: Mon, 05 Jun 2017 01:37:37 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] RMSD Matrix error
> Message-ID:
>         <CAMNuMATiG=
> MtnQwgMZF3r+sa-b2qAo38ywgW4x9HgpLUTFuyag at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *On Sun, Jun 4, 2017 at 4:08 PM Apramita Chand <apramita.chand at gmail.com
> <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
>
>
>
> yours sincerely,
> Apramita
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>