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>> 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. I'm not sure if you can pick
up using mdrun -cpi if the settings have changed, but you can try.
-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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