[gmx-users] Analyzing trajectory file always stops.

[yamashita.ryoto.82s at st.kyoto-u.ac.jp]

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

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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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