[gmx-users] WARNING: Incomplete frame

[Brett]

Dear Justin,



Will you please write out the restart command for me? I am afraid without your written command I cannot do it.


Brett









At 2016-04-05 22:06:57, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 4/5/16 10:04 AM, Brett wrote:
>> Dear Justin,
>>
>> WIll you please give a reply for the following question? Most probably I need to restart my MD from the beginning?
>>
>
>Restart from the last checkpoint and use -cpi -append.  mdrun will overwrite the 
>broken frames.  No need for trjcat, trjconv, etc.
>
>-Justin
>
>> Brett
>>
>>
>>
>>
>>
>>
>>
>> At 2016-04-05 17:18:31, "Brett" <brettliu123 at 163.com> wrote:
>>
>> Dear All,
>>
>>
>> After energy minimization and equilibration, I started a 10 ns production MD. By accident the production MD stopped at 450 ps (which produced md_0_1.trr), and I continue the production MD from the previous 450 ps point (which produced md_0_1_from0.45to10ns.trr).
>>
>>
>> Then by gmx trjcat -f md_0_1.trr md_0_1_from0.45to10ns.trr -b 2330 -e 2331 -o md_0_12330psto2332ps.trr, I tried to get 2330-2331 frame trr file. However although I got the  md_0_12330psto2332ps.trr, GROMAS gave a strong warning message:
>> WARNING: Incomplete frame: nr 234 time 468
>>
>>
>> Will you please advise whether my " md_0_1_from0.45to10ns.trr" was totally broken and whether I need to restart my production MD? And why I got the incomplete frame?
>>
>>
>> Brett
>>
>>
>>
>>
>>
>>
>>
>>
>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
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