[gmx-users] HELP:how could the simulation restarted from md*_prev.cpt rather than the md*.cpt

Justin Lemkul jalemkul at vt.edu
Sun Oct 30 01:42:37 CEST 2016



On 10/28/16 11:23 PM, 张慧玲 wrote:
>
> Hi, Justin I have 17 replicas, so I got {md0.cpt,md0_prev.cpt},   ......{md16.cpt,md16_prev.cpt}. Then I told gromacs to restart from the _prev.cpt using the following command:  mpirun -np 17 mdrun -deffnm md -multi 17 -noddcheck -replex 50000 -nsteps 100000000 -cpi md_prev
> However, it seems that Gromacs neglect the cpi option and rerun from step 0...
>

It may not be possible to automatically restart a REMD series from previous 
checkpoints.  Why do you need to start from a previous point rather than the 
most recent?  If you must restart from md*_prev.cpt, you may have to rename the 
files (e.g. just copy md*_prev.cpt to md*.cpt).

-Justin

>
>> On 10/26/16 11:05 PM, ??? wrote:
>>> Hi?
>>>     I have 17 replicas for a simulation, and Gromacs outputs two cpt files for each replica: md*_prev.cpt and md*.cpt
>>>     I know I can restart the simulation from checkpoint using the command "mpirun -np 17 mdrun-deffnm md -multi 17 -noddcheck -replex 50000 -nsteps 100000000 -cpi md", but how could I restart the simulatio from md*_prev.cpt rather than the md*.cpt?
>>>     Thanks a lot for your help.
>>>
>>
>> Tell mdrun to do that with -cpi md_prev.cpt instead of what you're doing now,
>> which is -cpi md.cpt
>>
>> -Justin
>>
>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>
>
>
>

-- 
==================================================

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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