[gmx-users] Restarting crashed simmulation.

neelam wafa neelam.wafa at gmail.com
Fri May 11 19:18:04 CEST 2018


*This is the message of gmx check for both the trajectories. I*t means that
trajectory is not continuous. Am I right?

*gmx check -f md_0_1.xtc*

Checking file md_0_1.xtc
Reading frame       0 time    0.000
# Atoms  67864
Precision 0.001 (nm)
Reading frame     200 time 2000.000


Item        #frames Timestep (ps)
Step           273    10
Time           273    10
Lambda           0
Coords         273    10
Velocities       0
Forces           0
Box            273    10

* gmx check -f traj_comp.xtc*

Checking file traj_comp.xtc
Reading frame       0 time 2720.000
# Atoms  67864
Precision 0.001 (nm)
Last frame         13 time 2850.000


Item        #frames Timestep (ps)
Step            14    10
Time            14    10
Lambda           0
Coords          14    10
Velocities       0
Forces           0
Box             14    10


On Fri, May 11, 2018 at 5:12 PM, neelam wafa <neelam.wafa at gmail.com> wrote:

> The previous command was :
>
> gmx mdrun -deffnm md_0_1
>
> I didn't ust -cpi falg .
>
> On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/11/18 12:52 PM, neelam wafa wrote:
>>
>>> I used this command:
>>> gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt
>>>
>>> But I think its not appending as new files are being generated with names
>>> state.cpt, state_prev.cpt and traj_comp.xtc
>>> while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc.
>>> Why has it happened ? I have checked log files but not able to infer a
>>> proper answer.
>>>
>>
>> The file names are contained within the .cpt file, and those are what
>> will be written. You haven't said what your previous command was, but the
>> use of -deffnm makes this much easier:
>>
>> gmx mdrun -deffnm md_0_1 -cpi
>>
>> You will always get clearly named files.
>>
>> If its not appened, will the final trajectory .xtc obtained cover the
>>> whole
>>> simmulation or I ll have to combine both results?
>>>
>>
>> Use gmx check.
>>
>> -Justin
>>
>>
>> Regards
>>>
>>>
>>> On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>> On 5/11/18 10:42 AM, neelam wafa wrote:
>>>>
>>>> Dear Sir Justin!
>>>>>
>>>>> I have restarted the simmulation but its producing a separate log file
>>>>> starting from the step where restarted. Is it normal response or there
>>>>> is
>>>>> some problem with my restart?
>>>>>
>>>>> That shouldn't happen; everything should be appended unless there was
>>>> some
>>>> problem (check the .log file itself and stdout/stderr for messages).
>>>> Appending is for convenience but there is no functional requirement for
>>>> it
>>>> (I never append on the fly by personal preference, I just concatenate
>>>> later).
>>>>
>>>> -Justin
>>>>
>>>>
>>>> Thanks in advance.
>>>>
>>>>> On Fri, May 11, 2018 at 12:06 PM, neelam wafa <neelam.wafa at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Thanks Sir Justin!
>>>>>
>>>>>> I have continued the simmulation from the last step.
>>>>>>
>>>>>> Regards
>>>>>>
>>>>>> On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>> On 5/10/18 7:08 AM, neelam wafa wrote:
>>>>>>>
>>>>>>> Hi gmx users!
>>>>>>>
>>>>>>>> I am running a 5ns md simmulation of a protein with 2500000 steps.
>>>>>>>> It
>>>>>>>> crashed at  1360000 steps due to some power problem. Now I want to
>>>>>>>> continue
>>>>>>>> this simmulation. In the manual following command is given:
>>>>>>>>
>>>>>>>> mdrun -s topol.tpr -cpi state.cpt
>>>>>>>>
>>>>>>>> but I am confused which file is state.cpt. I have got two cpt files
>>>>>>>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
>>>>>>>>
>>>>>>>> Look at the time stamps of the files and inspect their contents with
>>>>>>>>
>>>>>>> gmx
>>>>>>> check. You will see an obvious difference in what they contain. Also
>>>>>>> consult the mdrun help info, which specifically addresses your
>>>>>>> question.
>>>>>>>
>>>>>>> Also I did not get a md_1_0.gro file/ Is is due to incomplete
>>>>>>> simmulation?
>>>>>>> Yes, because that file is only produced from the last step.
>>>>>>>
>>>>>>> Also do I need to specify  -append flag or not? I am using version
>>>>>>> 5.1.5
>>>>>>> -append has been the default option for many years. Again, see the
>>>>>>> mdrun
>>>>>>> help description.
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>> --
>>>>>>> ==================================================
>>>>>>>
>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>> Assistant Professor
>>>>>>> Virginia Tech Department of Biochemistry
>>>>>>>
>>>>>>> 303 Engel Hall
>>>>>>> 340 West Campus Dr.
>>>>>>> Blacksburg, VA 24061
>>>>>>>
>>>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>>>> http://www.thelemkullab.com
>>>>>>>
>>>>>>> ==================================================
>>>>>>>
>>>>>>> --
>>>>>>> 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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>>>>>>> or
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>>>
>>>>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> 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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>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>>
>
>


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