[gmx-users] Finishing time donot showing

[XAvier Periole]

On Apr 20, 2010, at 7:39 PM, Bharath.K. Chakravarthi wrote:

> no i did not used -v flag at that command may be thats the mistake
> thank u Justin
>
> On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul <jalemkul at vt.edu>  
> wrote:
>
>
> Bharath.K wrote:
> I'm using gromacs-3.3.3 and here is the parameter
>
> ..
> ..
> nstxout             =  500
> nstvout             =  1000
> nstfout             =  0
> nstlist             =  100
This might not be the best choice! it is generally kept under 10! It  
depends on your
system/force field though....
> 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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>
>
>
> -- 
> Bharath.K.Chakravarthi
> Ph:9535629260
> -- 
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