Dear Sreemol,
In my opinion, you cannot have this information from files produced by
sander, in opposition to Gromacs.
You can still estimate it if you know the required time to produce a
certain number of steps using a constant CPU number and of course the
number of steps you are about to produce.
Also, you can find the current step during a production with sander
using tail command like :
tail -f [current_prod_file].out
It will print and update the end of this file, giving you something like
Bill already shown us.
Regards
Charlotte
Le 31/03/2016 16:27, Sreemol G a écrit :
> We are getting wall clock time only after the simulation ends. At the time
> of starting simulation, mdout file shows starting wall clock time. Like
> that is there any way to find the simulation end time once after starting
> the run??
> For example in case of gromacs we have command to show the time of
> completion of run. After starting the simulation it will show in the
> terminal itself, when will it end.
> On 31-Mar-2016 1:11 pm, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
>
>> Or if you mean the wall clock time when the simulation ended, the very
>> end of mdout will have it if the job ended ok:
>>
>> | Job began at 17:38:14.598 on 07/09/2015
>> | Setup done at 17:38:14.648 on 07/09/2015
>> | Run done at 17:45:12.982 on 07/09/2015
>>
>>
>> Bill
>>
>> On 3/31/16 12:35 AM, Bill Ross wrote:
>>> If the end of your mdout file does not have the info, either your job is
>>> still running or it crashed. E.g. something like this:
>>>
>>>
>>> NSTEP = 99900 TIME(PS) = 99.900 TEMP(K) = 294.59 PRESS
>> = 0.0
>>> Etot = 78.5037 EKtot = 560.2250 EPtot =
>> -481.7212
>>> BOND = 226.8325 ANGLE = 320.0852 DIHED =
>> 473.5326
>>> 1-4 NB = 170.0425 1-4 EEL = -363.2045 VDWAALS =
>> -291.2953
>>> EELEC = -1017.7143 EHBOND = 0.0000 RESTRAINT =
>> 0.0000
>> ------------------------------------------------------------------------------
>>> | RE_POSITION Moving by 0.349107 0.073865 0.343467
>>>
>>> NSTEP = 100000 TIME(PS) = 100.000 TEMP(K) = 293.27 PRESS
>> = 0.0
>>> Etot = 175.5232 EKtot = 557.7171 EPtot =
>> -382.1939
>>> BOND = 203.7967 ANGLE = 338.2706 DIHED =
>> 472.1763
>>> 1-4 NB = 165.3561 1-4 EEL = -372.1209 VDWAALS =
>> -282.5376
>>> EELEC = -907.1351 EHBOND = 0.0000 RESTRAINT =
>> 0.0000
>> ------------------------------------------------------------------------------
>>>
>>> A V E R A G E S O V E R 100000 S T E P S
>>>
>>>
>>> NSTEP = 100000 TIME(PS) = 100.000 TEMP(K) = 299.30 PRESS
>> = 0.0
>>> Etot = -51.7776 EKtot = 569.1930 EPtot =
>> -620.9707
>>> BOND = 226.4098 ANGLE = 330.2340 DIHED =
>> 469.2143
>>> 1-4 NB = 167.2158 1-4 EEL = -348.8599 VDWAALS =
>> -304.3686
>>> EELEC = -1160.8161 EHBOND = 0.0000 RESTRAINT =
>> 0.0000
>> ------------------------------------------------------------------------------
>>>
>>> Bill
>>>
>>>
>>> On 3/30/16 11:58 PM, Sreemol G wrote:
>>>> Is there any command in amber to display the completion time of
>>>> simulation?? md.out file is showing only the start time. Where and how
>> can
>>>> I find the end time??
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--
Charlotte Rieux
PhD student 2nd year
B. Castaing's team : "DNA repair : structural and functional approaches"
Centre de Biophysique Moléculaire
Rue Charles Sadron
45701 Orléans Cedex 2
Tel: +33 (0)2 38 25 55 68
Web site : http://cbm.cnrs-orleans.fr/
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Received on Thu Mar 31 2016 - 08:00:03 PDT
