[gmx-users] WARNING: Incomplete frame

[Justin Lemkul]

On 4/5/16 10:19 AM, Brett wrote:
> Dear Justin,
>
>
>
> Will you please write out the restart command for me? I am afraid without your written command I cannot do it.
>

Have you searched the archive?  Have you read any recent posts to this list?  I 
actually responded to someone else with the exact problem within the last hour.

-Justin

>
> Brett
>
>
>
>
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>
>
>
> 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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-- 
==================================================

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

==================================================