Re: [gmx-users] WARNING: Incomplete frame

2016-04-05 Thread 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"  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"  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
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
>-- 
>Gromacs Users mailing list
>
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Re: [gmx-users] WARNING: Incomplete frame

2016-04-05 Thread 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









At 2016-04-05 22:06:57, "Justin Lemkul"  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"  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

jalem...@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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] WARNING: Incomplete frame

2016-04-05 Thread Brett 
Dear Justin,

WIll you please give a reply for the following question? Most probably I need 
to restart my MD from the beginning?

Brett







At 2016-04-05 17:18:31, "Brett"  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






 
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Re: [gmx-users] WARNING: Incomplete frame

2016-04-05 Thread Justin Lemkul 



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"  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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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