[gmx-users] 答复: -extend problem

Fri Jul 4 04:19:14 CEST 2014

Dear gromacs users:
Can anyone tell me why  the total potential energy initially rises rapidly after which it relaxes again during a MD simulaiton? Thanks.

Best regards,
________________________________________
发件人: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> 代表 gromacs query <gromacsquery at gmail.com>
发送时间: 2014年7月4日 7:56
收件人: Discussion list for GROMACS users
主题: Re: [gmx-users] -extend problem

Hi

Sorry I think I found the error. I was using wrong name of -cpi file. But
its strange that mdrun does not  complain even if it could not find the
file and it still ran the job.

On Fri, Jul 4, 2014 at 12:31 AM, gromacs query <gromacsquery at gmail.com>
wrote:

> Hi Justin
>
> Indeed this key word 'Reading checkpoint file" is missing. I noted that I
> used same command in CPU (for other system) it was working fine. But now am
> running on GPU with same command and cpt file is not read. Dont know whats
> happening. Please suggest
>
> regards
>
>
> On Thu, Jul 3, 2014 at 11:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/3/14, 6:51 PM, gromacs query wrote:
>>
>>> 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?
>>>
>>>
>> If the .cpt file was read, it will say "Reading checkpoint file" just
>> after the input settings list and before the DD information.
>>
>>
>> -Justin
>>
>>
>>> 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
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/
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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/
>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>
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>>>> * For (un)subscribe requests visit
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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/
>> Support/Mailing_Lists/GMX-Users_List before posting!
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>>
>
>
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