On 4/27/12 12:09 PM, Steven Neumann wrote:
On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
On 4/27/12 11:34 AM, Steven Neumann wrote:
On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
On 4/27/12 11:22 AM, Steven Neumann wrote:
Dear Gmx Users,
I am running 2 us simulation in implicit solvent model:
define = -DPOSRES
integrator = sd ; leap-frog integrator
nsteps = 500000000 ; 0.004 * 500000000= 2 us
dt = 0.004 ; 4 fs
; Output control
nstxout = 0
nstxtcout = 50000 ; xtc compressed trajectory output
every 2 ps
nstenergy = 10000 ; save energies every 2 ps
nstlog = 10000 ; update log file every 2 ps
How come my trajectory (trr) is being created and takes 80 GB?
The default for nstvout is 100, so you're likely getting very
frequent
output of velocities into the .trr file.
-Justin
Thank you
This job crashed due to the quota exceeded. If change my mdp file (with
additional nstvout=0) using tpbconv and run it from the checkpoint
file it
should work then with no trr file?
If you need to change the .mdp file, you can't use tpbconv; use grompp to
generate a new .tpr file and submit the new job.
So if I will create new mdp file (with additional nstvout=0 to get rid of trr
files) and use:
mdrun -s new.tpr -cpi last.cpt
Will I continue from the checkpoint?
That's the question I posed below...
I'm not sure if you can pick up using mdrun -cpi if the settings have
changed, but you can try.
Yes you can, from 4.0 you do not have to specify -append just -cpi file if the
job crashed.
I am aware of checkpointing, but what I'm not sure of is if you change output
options (or others) mid-stream, if the checkpointing mechanism will complain,
particularly due to the changes in the .trr content. You'll have to try and see.
-Justin
--
========================================
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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