[gmx-users] -extend problem

[Justin Lemkul]

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

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