[gmx-users] Re:Re: Incomplete header: nr 3078 time 9408
Dechang Li
li.dc06 at gmail.com
Sun Nov 11 13:10:19 CET 2007
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>Today's Topics:
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> 1. Re: Incomplete header: nr 3078 time 9408 (David van der Spoel)
> 2. Re: trjorder does not write trajectory file (Dmytro Kovalskyy)
>
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>----------------------------------------------------------------------
>
>Message: 1
>Date: Sun, 11 Nov 2007 09:41:35 +0100
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] Incomplete header: nr 3078 time 9408
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4736C03F.7020100 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=UTF-8; format=flowed
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>Dechang Li wrote:
>> Dear all,
>>
>> I used Gromacs-3.3.1 to do a simulation. When it finished, I used
>> command "g_dist" to calculate two groups distance VS time. But at time
>> 9408ps, it stopped and showed " Incomplete header: nr 3078 time 9408".
>> My simulation is 12ns longer. What is the problem? How can I resolve it?
>>
>>
>start by testing the trajectory with gmxcheck
I did what you said. Following is the message:
Reading frame 3000 time 9254.000 Warning at frame 3077. Velocities for atom 11896 are large (52568.4)
Warning at frame 3077. Velocities for atom 11896 are large (7.68295e+31)
Warning at frame 3077. Velocities for atom 11896 are large (2.75578e+23)
Warning at frame 3077. Velocities for atom 11901 are large (9410)
WARNING: Incomplete header: nr 3078 time 9408
Item #frames Timestep (ps)
Step 3078 2
Time 3078 2
Lambda 3078 2
Coords 3078 2
Velocities 3078 2
Forces 0
Box 3078 2
Did it mean my simulation was failed? But I have checked the energy file "ener.edr", too. The energy file
seems fine. How did it happen? Can I use the date after time 9254ps?
>> Best regards,
>>
>> 2007-11-11
>> 　　　　　　　　
>>
>> =========================================
>> Dechang Li, PhD Candidate
>> Department of Engineering Mechanics
>> Tsinghua University
>> Beijing 100084
>> PR China
>>
>> Tel: +86-10-62773779(O)
>> Email: li.dc06 at gmail.com
>> =========================================　　　　　
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>
>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: 46 18 471 4205 fax: 46 18 511 755
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>------------------------------
>
>Message: 2
>Date: Sun, 11 Nov 2007 13:01:19 +0200 (EET)
>From: "Dmytro Kovalskyy" <dikov at imbg.org.ua>
>Subject: Re: [gmx-users] trjorder does not write trajectory file
>To: "Justin A. Lemkul" <jalemkul at vt.edu>
>Cc: gmx-users at gromacs.org
>Message-ID:
> <62554.213.160.133.126.1194778879.squirrel at webmail.imbg.org.ua>
>Content-Type: text/plain;charset=utf-8
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>> It works fine for me under 3.3.1 - what command line are you issuing?
>trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5
>>
>> -Justin
>>
>> Quoting Dmytro Kovalskyy <dikov at imbg.org.ua>:
>>
>>>
>>> Trjorder does not write trajectory file, only nshell.xvg
>>>
>>> This is true for 3.3.2 and 3.3.1 versions.
>>>
>>> Dima
>>>
>>>
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>>
>>
>>
>> =========================================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul at vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>
>> =========================================================
>>
>>
>> !DSPAM:47367e03304461801161890!
>>
>>
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