[gmx-users] energy file

[Justin A. Lemkul]

jayant james wrote:
> Hi!
> Thanks for your reply.
> I am having an on going simulation the md.log file states that it has 
> written 875ps but the energy file data for only 662 ps!! this is brand 
> new machine and is so there is no problem of running out of space. I am 
> appending my pr.mdp file please take a look if its some thing to do with 
> parameters and kindly suggest modifications if needed.

Data is not written continuously, it is buffered.  So, there can be some 
difference between the .log, .edr, .trr, etc during the simulation.

-Justin

> Thanks
> JJ
> title               =  Yo
> cpp                 =  /usr/bin/cpp
> define              = -DDISRES
> constraints         =  none
> ;constraint_algorithm =  lincs
> ;lincs_order         =  4
> integrator          =  md
> dt                  =  0.001    ; ps !
> nsteps              =  1000000  ; total 1.0ns.
> nstcomm             =  1
> nstxout             =  5000
> nstvout             =  5000
> nstfout             =  5000
> nstlog              =  5000
> nstenergy           =  5000
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> coulombtype         =  PME
> rcoulomb            =  1.0
> vdwtype             =  cut-off
> rvdw                =  1.4
> fourierspacing      = 0.12
> fourier_nx          = 0
> fourier_ny          = 0
> fourier_nz          = 0
> pme_order           = 4
> ewald_rtol          = 1e-5
> optimize_fft        = yes
> disre               =  simple
> disre_weighting     =  equal
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  V-rescale
> tc-grps             =  Protein    Non-Protein
> tau_t               =  0.1        0.1
> ref_t               =  300        300
> ; Energy monitoring
> energygrps          =  Protein     Non-Protein
> ; Pressure coupling is not on
> Pcoupl              =  parrinello-rahman
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> "pr.mdp" 52L, 
> 1481C                                                                                                                        
> 38,1          Top
> 
> 
> 
> 
> On Wed, Feb 25, 2009 at 11:03 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     jayant james wrote:
> 
>         Hi!
>         I ran a simulation for 1ns (it was a continious run) and when I
>         analyse the system energy, I find that the energy file has input
>         till only 500pico seconds. Now that I want to extend my
>         simulations I am in a fix!! What could be going wrong? I am
>         using GMX version 3.3.3.
> 
> 
>     Maybe your file system became full, or your cluster file system was
>     no longer accessible to the simulation node, or the simulation was
>     interrupted before it completed flushing the buffers. Whatever
>     happened, GROMACS did not terminate normally, because if there were
>     any relevant .edr parameters to save at simulation end, it would
>     have done so.
> 
>     If you consult the wiki, you will see some strategies for recovering
>     from here.
> 
>     Mark
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> 
> 
> 
> -- 
> Jayasundar Jayant James
> 
> www.chick.com/reading/tracts/0096/0096_01.asp 
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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