[gmx-users] energy file

[jayant james]

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.
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>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)
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