[gmx-users] Analyzing trajectory file always stops.

[Mark Abraham]

Hi,

That usually means you are working in a filesystem like FAT32 that cannot
access files greater than 2GB. If so, try a real one :-)

Mark

On Sun, 24 Jul 2016 12:53 yamashita.ryoto.82s at st.kyoto-u.ac.jp <
yamashita.ryoto.82s at st.kyoto-u.ac.jp> wrote:

>
> Dear Mr.Lemkul
> >How large is your trajectory?  How much memory do you have >available?
> Does
> >reducing the frame interval with trjconv work?
>
> Thank you for commenting.
> My trajectory file is 109GB.(10000000 steps)
> According to the command vmstat, avm is 1044MB( and fre is 616MB).
> reducing the frame interval with trjconv also stops
> It stops at the same Reading frame 1100.
> (I'm sorry,  I correct the wrong information that analyzing stops at not
> two thirds but one 10000th of my file.)
> the command is
> gmx_mpi_d trjconv -f oligomer.tpr.trr -s oligomer.tpr -dt 10000 -o test.trr
>
> Thanks,
> Yamashita
>
> ________________________________
> 差出人: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> が Justin Lemkul <
> jalemkul at vt.edu> の代理で送信
> 送信日時: 2016年7月22日 20:34:31
> 宛先: gmx-users at gromacs.org
> 件名: Re: [gmx-users] Analyzing trajectory file always stops.
>
>
>
> On 7/21/16 9:19 PM, yamashita.ryoto.82s at st.kyoto-u.ac.jp wrote:
> > Dear all.
> > I have a trouble when analyzing my trajectory file.
> > I want to calculate the radius of gyration of oligomer.But when
> calculating the radius of gyration, the calculations always stop at about
> two thirds of my trajectory file.
> > Could you tell me what is happening if you know?
> >
>
> How large is your trajectory?  How much memory do you have available?  Does
> reducing the frame interval with trjconv work?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland.edu/~jalemkul>
> mackerell.umaryland.edu
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