[gmx-users] -extend problem

[gromacs query]

Hi

forgive my ignorance but I could not find whether my cpt was read
successfully or not as I dont see anything in log file as which files were
taken as input. Or any keyword I should search for?


On Thu, Jul 3, 2014 at 11:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/3/14, 6:34 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> Sorry, I should have mentioned that I used -cpi : here is my mdrun command
>> after tpbconv
>>
>>
>> tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250
>>
>>
>> mdrun_mpi -s npt_new.tpr -o traj.trr -e ener.edr -c conf_prev.gro -g
>> md.log
>> -cpo state_new.cpt -cpi state_prev.cpt
>>
>>
> The .log file will have details of what is going on.  If the run proceeded
> from 0-500 ps, the input .cpt file was not read.
>
> -Justin
>
>
>
>> On Thu, Jul 3, 2014 at 11:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 7/3/14, 6:05 PM, gromacs query wrote:
>>>
>>>  Hi All
>>>>
>>>> I generated my npt.tpr with:
>>>>
>>>>
>>>> tinit=0
>>>>
>>>> dt=0.002
>>>>
>>>> nsteps=125000
>>>>
>>>> I am trying to extend simulation for 250 ps like this:
>>>>
>>>> tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250
>>>>
>>>>
>>>> But when I used this npt_new.tpr simulation it ran for 500 ps. Have I
>>>> missed something?
>>>>
>>>>
>>>>  If you simply pass npt_new.tpr to mdrun, that's what you should expect.
>>>   If you use mdrun -cpi to pick up from the last checkpoint at 250 ps,
>>> then
>>> you'll get an extended run instead of one that starts from t = 0.
>>>
>>>
>>>
>>>  Also one more thing why the Gromacs user archive search engine does not
>>>> work like before?
>>>>
>>>>
>>>>  The Nabble archive?  It was disabled months ago.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> 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 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>
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>