[gmx-users] Finishing time donot showing

[Justin A. Lemkul]

Bharath.K wrote:
> I'm using gromacs-3.3.3 and here is the parameter
> 
> ..
> ..
> nstxout             =  500
> nstvout             =  1000
> nstfout             =  0
> nstlist             =  100
> nstlog              =  100
> nstenergy           =  10
> nstxtcout           =  500
> ..
> ..
> 
>  for writing trajectories in .mdp file and what is check point file and 
> -cpi file.cpt ...
> i did not get u.... :(
> 

This is why stating your Gromacs version at the outset is useful.  Checkpointing 
was introduced in Gromacs 4.0, so you won't be able to use it.

You also have not answered my first question.  What is your mdrun command line? 
  Did you use the -v flag?  If not, you will not get any information about 
completion time.  There is nothing that the .mdp options or tpbconv will do for 
you as far as completion time is concerned.

-Justin

> On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole <x.periole at rug.nl> 
> wrote:
> 
>>
>>>
>>> >tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000
>>> this shows last step before crashing and starts from there until 1000
>>>
>>
>>> then
>>>
>>> >mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log -
>>> e minim_ener_01.edr
>>>
>>
>> Nothing seem particularly wrong! May be you write your trajectory file
>> too often! Did the original the indicated the same amount of data to be
>> written?
>>
>> which version of gmx you are using? actually using the check point
>> file is relatively easy (-cpi fie.cpt to add to mdrun) and does all
>> the work for you!
>>>
>>
>>
>>>
>>> On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole <x.periole at rug.nl>
>>> wrote:
>>>
>>> On Apr 20, 2010, at 9:14 AM, Bharath.K wrote:
>>>
>>> Hello all....
>>> i got a system crash at some steps..
>>> after creating the new .trr file using command tpbconv
>>> trr file with tpbconv? you mean tpr?
>>> and running MDS
>>> what is MDS?
>>>
>>> by mdrun command the approximate finishing time is not showing.....
>>> and also a warning is showing as
>>>
>>> WARNING: this run may generate approximately 4583292 Mb of data....
>>> That is a bit enormous
>>>
>>>
>>> is there any changes that i should do while giving the command and
>>> can i continue with this warning.....
>>> Which exact command did you use?
>>>
>>>
>>>
>>> -- 
>>> Bharath.K
>>> Ph-9535629260
>>> -- 
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>>>
>>> -- 
>>> Bharath.K.Chakravarthi
>>> Ph:9535629260
>>> -- 
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>>
> 
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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